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

#include <ActionWithVessel.h>

Inheritance diagram for PLMD::vesselbase::ActionWithVessel:
Inheritance graph
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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...
 
StoreDataVesselbuildDataStashes (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 DependenciesgetDependencies () 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...
 
VesselgetPntrToVessel (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...
 
VesselgetVesselWithName (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

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

Protected Member Functions

BridgeVesseladdBridgingVessel (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...
 
StoreDataVesselmydata
 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...
 
bool active
 Switch to activate Action on this step. More...
 
Dependencies after
 Actions on which this Action depends. 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...
 
bool doCheckPoint
 
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...
 
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...
 
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...
 
const std::string name
 Name of the directive in the plumed.dat file. 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::set< std::string > options
 Option that you might have enabled. More...
 
std::vector< unsigned > partialTaskList
 The list of currently active tasks. More...
 
int replica_index
 
bool restart
 
bool serial
 Do all calculations in serial. More...
 
Stopwatchstopwatch =*stopwatch_fwd
 The stopwatch that times the different parts of the calculation. More...
 
ForwardDecl< Stopwatchstopwatch_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...
 
double update_from
 Update only after this time. More...
 
double update_until
 Update only until this time. 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::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.

◆ 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::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.

◆ 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

◆ 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.

Reimplemented in PLMD::gridtools::ConvertToFES.

◆ 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

◆ 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.

Implemented in PLMD::analysis::Histogram, PLMD::multicolvar::XDistances, PLMD::multicolvar::XYTorsion, PLMD::multicolvar::Distances, PLMD::pamm::PAMM, PLMD::gridtools::FindContour, PLMD::multicolvar::XYDistances, PLMD::multicolvar::AlphaBeta, PLMD::analysis::Average, PLMD::multicolvar::LocalAverage, PLMD::multicolvar::MultiColvarDensity, PLMD::multicolvar::Angles, PLMD::multicolvar::XAngles, PLMD::multicolvar::DistanceFromContour, PLMD::analysis::AnalysisBase, PLMD::multicolvar::CoordinationNumbers, PLMD::multicolvar::DihedralCorrelation, PLMD::gridtools::FourierTransform, PLMD::mapping::Mapping, PLMD::multicolvar::NumberOfLinks, PLMD::secondarystructure::SecondaryStructureRMSD, PLMD::multicolvar::Torsions, PLMD::gridtools::ConvertToFES, PLMD::multicolvar::Bridge, PLMD::multicolvar::InPlaneDistances, PLMD::multicolvar::BridgedMultiColvarFunction, PLMD::adjmat::ActionWithInputMatrix, PLMD::gridtools::InterpolateGrid, PLMD::multicolvar::Density, PLMD::pamm::HBPammHydrogens, PLMD::multicolvar::MultiColvarCombine, PLMD::adjmat::ClusterAnalysisBase, PLMD::multicolvar::MultiColvarProduct, PLMD::gridtools::ContourFindingBase, PLMD::manyrestraints::ManyRestraintsBase, PLMD::gridtools::ActionWithIntegral, PLMD::crystallization::EnvironmentSimilarity, PLMD::crystallization::InterMolecularTorsions, PLMD::adjmat::AdjacencyMatrixBase, PLMD::crystallization::VectorMultiColvar, PLMD::crystallization::CubicHarmonicBase, and PLMD::crystallization::OrientationSphere.

◆ lockContributors()

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

◆ lockRequests()

virtual void PLMD::Action::lockRequests ( )
inlinevirtualinherited

◆ 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

◆ normalizeVectorDerivatives()

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

◆ 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

◆ 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::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 )
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::multicolvar::Torsions, and PLMD::crystallization::InterMolecularTorsions.

◆ 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

◆ update()

virtual void PLMD::Action::update ( )
inlinevirtualinherited

◆ 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.

◆ active

bool PLMD::Action::active
privateinherited

Switch to activate Action on this step.

◆ after

Dependencies PLMD::Action::after
privateinherited

Actions on which this Action depends.

◆ 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.

◆ doCheckPoint

bool PLMD::Action::doCheckPoint
privateinherited

◆ 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

◆ label

std::string PLMD::Action::label
privateinherited

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

◆ line

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

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
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.

◆ name

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

Name of the directive in the plumed.dat file.

◆ 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.

◆ options

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

Option that you might have enabled.

◆ 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.

◆ replica_index

int PLMD::Action::replica_index
privateinherited

◆ restart

bool PLMD::Action::restart
privateinherited

◆ 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.

◆ update_from

double PLMD::Action::update_from
privateinherited

Update only after this time.

◆ update_until

double PLMD::Action::update_until
privateinherited

Update only until this time.

◆ weightHasDerivatives

bool PLMD::vesselbase::ActionWithVessel::weightHasDerivatives
protected

Does the weight have derivatives.


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