Public Types | Public Member Functions | Static Public Member Functions | Public Attributes | Protected Member Functions | Protected Attributes | Friends | List of all members
PLMD::analysis::AnalysisBase Class Referenceabstract


This is the abstract base class to use for implementing new methods for analyzing the trajectory. More...

#include <AnalysisBase.h>

Inheritance diagram for PLMD::analysis::AnalysisBase:
Inheritance graph
[legend]

Public Types

typedef std::vector< Action * > Dependencies
 

Public Member Functions

 AnalysisBase (const ActionOptions &)
 
virtual void activate ()
 Set action to active. More...
 
void addComponent (const std::string &name)
 Add a value with a name like label.name. More...
 
void addComponentWithDerivatives (const std::string &name)
 Add a value with a name like label.name that has derivatives. More...
 
void addDependency (Action *)
 Specify that this Action depends on another one. More...
 
void addForcesOnArguments (const std::vector< double > &forces)
 Add forces to arguments (used in apply) More...
 
void addValue ()
 Add a value with the name label. More...
 
void addValueWithDerivatives ()
 Add a value with the name label that has derivatives. More...
 
void allowToAccessGlobalForces ()
 Allow calls to modifyGlobalForce() More...
 
void apply () override
 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...
 
void applyForces ()
 
virtual void beforeUpdate ()
 Before Update. More...
 
double bringBackInPbc (int i, double d1) const
 Takes one value and brings it back into the pbc of argument i. More...
 
StoreDataVesselbuildDataStashes (ActionWithVessel *actionThatUses)
 Ensure that data required in other vessels is stored. More...
 
void calculate () override
 Calculate and apply do nothing all analysis is done during update step. More...
 
void calculateAtomicNumericalDerivatives (ActionWithValue *a, const unsigned &startnum)
 Numerical derivative routine to use when using Actions that inherit from BOTH ActionWithArguments and ActionAtomistic. More...
 
void calculateFromPDB (const PDB &)
 Calculate the action given a pdb file as input. More...
 
void calculateNumericalDerivatives (ActionWithValue *a=NULL) override
 Perform calculation using numerical derivatives N.B. More...
 
void changeBox (const Tensor &newbox)
 Change the box shape. More...
 
virtual void checkFieldsAllowed ()
 
virtual bool checkNeedsGradients () const
 Check if the action needs gradient. More...
 
bool checkNumericalDerivatives () const override
 Check if numerical derivatives should be used. 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 clearDerivatives ()
 Clear the derivatives of values wrt parameters. More...
 
void clearInputForces ()
 Clear the forces on the values. More...
 
virtual void clearOptions ()
 
void clearOutputForces ()
 
void componentIsNotPeriodic (const std::string &name)
 Set your value component to have no periodicity. More...
 
void componentIsPeriodic (const std::string &name, const std::string &min, const std::string &max)
 Set the value to be periodic with a particular domain. More...
 
ValuecopyOutput (const std::string &name) const
 Return a pointer to the value with name (this is used to retrieve values in other PLMD::Actions) You should NEVER use this routine to refer to the components of your PLMD::Action. More...
 
ValuecopyOutput (const unsigned &n) const
 Return a pointer to the value with this number (this is used to retrieve values in other PLMD::Actions) You should NEVER use this routine to refer to the components of your PLMD::Action. More...
 
virtual void deactivate ()
 Set action to inactive. More...
 
bool derivativesAreRequired () const
 Are derivatives required for this quantity. More...
 
double difference (int, double, double) const
 Takes the difference taking into account pbc for arg i. More...
 
virtual bool dissimilaritiesWereSet () const
 Ensures that dissimilarities were set somewhere. More...
 
virtual void doJobsRequiredBeforeTaskList ()
 Do any jobs that are required before the task list is undertaken. More...
 
virtual bool doNotCalculateDerivatives () const
 Are we not calculating derivatives. More...
 
void doNotForce ()
 Skip atom forces - use with care. More...
 
void doNotRetrieve ()
 Skip atom retrieval - use with care. More...
 
void error (const std::string &msg) const
 Crash calculation and print documentation. More...
 
bool exists (const std::string &name) const
 Check if a value with a particular name is present. 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...
 
AtomNumber getAbsoluteIndex (int i) const
 Get the absolute index of an atom. More...
 
virtual const std::vector< AtomNumber > & getAbsoluteIndexes () const
 Get the vector of absolute indexes. More...
 
unsigned getActiveTask (const unsigned &ii) const
 Get the ith of the currently active tasks. More...
 
double getArgument (const unsigned n) const
 Returns the value of an argument. More...
 
virtual std::vector< Value * > getArgumentList ()
 Overwrite getArguments so we get arguments from underlying class. More...
 
std::vector< std::string > getArgumentNames ()
 Get the list of argument names in the base. More...
 
virtual const std::vector< Value * > & getArguments () const
 Returns an array of pointers to the arguments. More...
 
virtual const std::vector< AtomNumber > & getAtomIndexes () const
 Get the indices of the atoms that have been stored. More...
 
const TensorgetBox () const
 Get box shape. More...
 
double getCharge (int i) const
 Get charge of i-th atom. More...
 
std::string getComponentsList () const
 get a string that contains all the available components More...
 
std::vector< std::string > getComponentsVector () const
 get a vector that contains the label for all the components 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...
 
virtual unsigned getDataPointIndexInBase (const unsigned &idata) const
 Return the index of the data point in the base class. More...
 
const DependenciesgetDependencies () const
 Return dependencies. More...
 
virtual double getDissimilarity (const unsigned &i, const unsigned &j)
 Get the squared dissimilarity between two reference configurations. More...
 
virtual std::string getDissimilarityInstruction () const
 Get the information on how dissimilarities were calculated for output PDB. More...
 
virtual std::string getDocumentation () const
 
const double & getEnergy () const
 Get energy. More...
 
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...
 
const VectorgetGlobalPosition (AtomNumber) const
 Get position of i-th atom (access by absolute AtomNumber). 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...
 
double getMass (int i) const
 Get mass of i-th atom. More...
 
virtual std::string getMetricName () const
 Get the name of the metric that is being used. More...
 
const std::string & getName () const
 Returns the name. More...
 
virtual double getNormalization () const
 Return the normalisation constant for the calculation. More...
 
virtual unsigned getNumberOfArguments () const
 Returns the number of arguments. More...
 
unsigned getNumberOfAtoms () const
 Get number of available atoms. More...
 
int getNumberOfComponents () const
 Returns the number of values defined. More...
 
virtual unsigned getNumberOfDataPoints () const
 Return the number of data points. More...
 
unsigned getNumberOfDerivatives () override
 
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...
 
double getOutputQuantity (const unsigned j) const
 Get the value of one of the components of the PLMD::Action. More...
 
double getOutputQuantity (const std::string &name) const
 Get the value with a specific name (N.B. if there is no such value this returns zero) More...
 
const PbcgetPbc () const
 Get reference to Pbc. More...
 
ValuegetPntrToArgument (const unsigned n)
 Return a pointer to specific argument. More...
 
VesselgetPntrToVessel (const unsigned &i)
 Get a pointer to the ith vessel. More...
 
const VectorgetPosition (int) const
 Get position of i-th atom (access by relative index) 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...
 
const std::vector< Vector > & getPositions () const
 Get the array of all positions. More...
 
double getProjection (unsigned i, unsigned j) const
 Get the scalar product between the gradients of two variables. More...
 
bool getRestart () const
 Return true if we are doing a restart. More...
 
long int getStep () const
 Return the present timestep. More...
 
virtual DataCollectionObjectgetStoredData (const unsigned &idata, const bool &calcdist)
 Get a reference configuration (in dimensionality reduction this returns the projection) More...
 
int getStride () const
 Get the stride. 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...
 
unsigned getTotAtoms () const
 Get total number of atoms, including virtual ones. More...
 
const std::set< AtomNumber > & getUnique () const
 
const std::set< AtomNumber > & getUniqueLocal () const
 
VesselgetVesselWithName (const std::string &mynam)
 These are overwritten in MultiColvarFunction. More...
 
virtual double getWeight (const unsigned &idata)
 Return the weight of the ith point. More...
 
void interpretArgumentList (const std::vector< std::string > &c, std::vector< Value *> &arg)
 Convert a list of argument names into a list of pointers to the values. More...
 
void interpretAtomList (std::vector< std::string > &strings, std::vector< AtomNumber > &t)
 Convert a set of read in strings into an atom list (this is used in parseAtomList) More...
 
bool isActive () const
 Check if action is active. More...
 
bool isOptionOn (const std::string &s) const
 Check if an option is on. More...
 
bool isPeriodic () override
 These overwrite things from inherited classes (this is a bit of a fudge) More...
 
void lockContributors ()
 
void lockRequests () override
 These are required because we inherit from both ActionAtomistic and ActionWithArguments. More...
 
void makeWhole ()
 Make atoms whole, assuming they are in the proper order. More...
 
double & modifyForceOnEnergy ()
 Get a reference to force on energy. More...
 
double & modifyForceOnExtraCV ()
 Get a reference to force on extraCV. More...
 
std::vector< Vector > & modifyForces ()
 Get a reference to forces array. More...
 
VectormodifyGlobalForce (AtomNumber)
 Get modifiable force of i-th atom (access by absolute AtomNumber). More...
 
PbcmodifyGlobalPbc ()
 Get modifiable PBC Should be used by action that need to modify the stored box. More...
 
VectormodifyGlobalPosition (AtomNumber)
 Get modifiable position of i-th atom (access by absolute AtomNumber). More...
 
TensormodifyGlobalVirial ()
 Get modifiable virial Should be used by action that need to modify the stored virial. More...
 
TensormodifyVirial ()
 Get a reference to virial array. More...
 
virtual void normalizeVector (std::vector< double > &vals) const
 These normalizes vectors and is used in StoreDataVessel. More...
 
virtual void normalizeVectorDerivatives (MultiValue &myvals) const
 
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 parseArgumentList (const std::string &key, std::vector< Value *> &args)
 Parse a list of arguments. More...
 
bool parseArgumentList (const std::string &key, int i, std::vector< Value *> &args)
 Parse a numbered list of arguments. More...
 
void parseAtomList (const std::string &key, std::vector< AtomNumber > &t)
 Parse a list of atoms without a numbered keyword. More...
 
void parseAtomList (const std::string &key, const int num, std::vector< AtomNumber > &t)
 Parse an list of atom with a numbred keyword. 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...
 
void pbcApply (std::vector< Vector > &dlist, unsigned max_index=0) const
 Applies PBCs to a seriens of positions or distances. More...
 
Vector pbcDistance (const Vector &, const Vector &) const
 Compute the pbc distance between two positions. More...
 
virtual void performAnalysis ()=0
 This actually performs the analysis. 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...
 
void readAtomsFromPDB (const PDB &pdb) override
 Read in an input file containing atom positions and calculate the action for the atomic configuration therin. 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 requestArguments (const std::vector< Value *> &arg)
 Setup the dependencies. More...
 
void requestAtoms (const std::vector< AtomNumber > &a, const bool clearDep=true)
 Request an array of atoms. More...
 
virtual void retrieveAtoms ()
 
virtual void retrieveDomain (std::string &min, std::string &max)
 What are the domains of the base quantities. More...
 
void runFinalJobs () override
 This calls the analysis to be performed in the final step of the calculation i.e. More...
 
void setForcesOnAtoms (const std::vector< double > &forcesToApply, unsigned ind=0)
 Add the forces to the atoms. More...
 
void setGradientsIfNeeded ()
 Calculate the gradients and store them for all the values (need for projections) More...
 
void setNotPeriodic ()
 Set your default value to have no periodicity. More...
 
virtual void setOption (const std::string &s)
 
void setPeriodic (const std::string &min, const std::string &max)
 Set the value to be periodic with a particular domain. More...
 
void setStride (const int &n)
 Set the value of the stride. More...
 
void setValue (Value *, double)
 Set the value. More...
 
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 turnOnDerivatives ()
 Activate the calculation of derivatives. More...
 
void unlockRequests () override
 
void update () override
 This will call the analysis to be performed. More...
 
void updateUniqueLocal ()
 updates local unique atoms More...
 
void useNumericalDerivatives ()
 This forces the class to use numerical derivatives. More...
 
virtual bool usingMemory () const
 Are we using memory in this calculation this affects the weights of points. 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 componentsAreNotOptional (Keywords &keys)
 Puts a message into the manual that the components always output. More...
 
static void noAnalyticalDerivatives (Keywords &keys)
 Insist that numerical derivatives should always be used for an action and make this fact appear in the manual. More...
 
static void registerKeywords (Keywords &keys)
 
static void useCustomisableComponents (Keywords &keys)
 The components in the action will depend on the user. More...
 

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...
 
void expandArgKeywordInPDB (PDB &pdb)
 This changes the arg keyword in the pdb file. 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...
 
ValuegetPntrToComponent (int i)
 Return a pointer to the component by index. More...
 
ValuegetPntrToComponent (const std::string &name)
 Return a pointer to the value by name. More...
 
ValuegetPntrToValue ()
 Get a pointer to the default value. 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 setExtraCV (const std::string &name)
 
void setLowMemOption (const bool &)
 Set that we are using low memory. More...
 
void setValue (const double &d)
 Set the default value (the one without name) More...
 
bool usingLowMem () const
 Are we using low memory. More...
 

Protected Attributes

Atomsatoms
 
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...
 
AnalysisBasemy_input_data
 The Analysis action that we are reusing data from. 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...
 

Friends

class ReadDissimilarityMatrix
 
class ReselectLandmarks
 

Detailed Description


This is the abstract base class to use for implementing new methods for analyzing the trajectory.

You can find information on how to use it to implement new analysis methods here.

Member Typedef Documentation

◆ Dependencies

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

Constructor & Destructor Documentation

◆ AnalysisBase()

PLMD::analysis::AnalysisBase::AnalysisBase ( const ActionOptions ao)
explicit

Member Function Documentation

◆ activate()

void PLMD::Action::activate ( )
virtualinherited

Set action to active.

◆ addBridgingVessel()

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

Add a bridging vessel to the list of vessels.

◆ addComponent()

void PLMD::ActionWithValue::addComponent ( const std::string &  name)
inherited

Add a value with a name like label.name.

◆ addComponentWithDerivatives()

void PLMD::ActionWithValue::addComponentWithDerivatives ( const std::string &  name)
inherited

Add a value with a name like label.name that has derivatives.

◆ addDependency()

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

Specify that this Action depends on another one.

◆ addForcesOnArguments()

void PLMD::ActionWithArguments::addForcesOnArguments ( const std::vector< double > &  forces)
inherited

Add forces to arguments (used in apply)

◆ addTaskToList()

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

Add a task to the full list.

◆ addValue()

void PLMD::ActionWithValue::addValue ( )
inherited

Add a value with the name label.

◆ addValueWithDerivatives()

void PLMD::ActionWithValue::addValueWithDerivatives ( )
inherited

Add a value with the name label that has derivatives.

◆ addVessel() [1/2]

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

Add a vessel to the list of vessels.

◆ addVessel() [2/2]

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

◆ allowToAccessGlobalForces()

void PLMD::ActionAtomistic::allowToAccessGlobalForces ( )
inlineinherited

Allow calls to modifyGlobalForce()

◆ apply()

void PLMD::analysis::AnalysisBase::apply ( )
inlineoverridevirtual

Apply an Action.

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

Implements PLMD::Action.

◆ applyBridgeForces()

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

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

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

◆ applyForces()

void PLMD::ActionAtomistic::applyForces ( )
inherited

◆ 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.

◆ bringBackInPbc()

double PLMD::ActionWithArguments::bringBackInPbc ( int  i,
double  d1 
) const
inlineinherited

Takes one value and brings it back into the pbc of argument i.

◆ buildDataStashes()

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

Ensure that data required in other vessels is stored.

◆ calculate()

void PLMD::analysis::AnalysisBase::calculate ( )
inlineoverridevirtual

Calculate and apply do nothing all analysis is done during update step.

Implements PLMD::Action.

◆ calculateAllVessels()

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

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

◆ calculateAtomicNumericalDerivatives()

void PLMD::ActionAtomistic::calculateAtomicNumericalDerivatives ( ActionWithValue a,
const unsigned &  startnum 
)
inherited

Numerical derivative routine to use when using Actions that inherit from BOTH ActionWithArguments and ActionAtomistic.

◆ 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::analysis::AnalysisBase::calculateNumericalDerivatives ( ActionWithValue a = NULL)
inlineoverridevirtual

Perform calculation using numerical derivatives N.B.

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

Reimplemented from PLMD::Action.

◆ changeBox()

void PLMD::ActionAtomistic::changeBox ( const Tensor newbox)
inherited

Change the box shape.

◆ checkFieldsAllowed()

virtual void PLMD::ActionWithValue::checkFieldsAllowed ( )
inlinevirtualinherited

Reimplemented in PLMD::piv::PIV, and PLMD::colvar::ContactMap.

◆ 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() [1/2]

bool PLMD::ActionWithValue::checkNumericalDerivatives ( ) const
inlineoverridevirtualinherited

Check if numerical derivatives should be used.

Reimplemented from PLMD::Action.

◆ checkNumericalDerivatives() [2/2]

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.

◆ clearDerivatives()

void PLMD::ActionWithValue::clearDerivatives ( )
virtualinherited

Clear the derivatives of values wrt parameters.

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

◆ clearInputForces()

void PLMD::ActionWithValue::clearInputForces ( )
inherited

Clear the forces on the values.

◆ clearOptions()

void PLMD::Action::clearOptions ( )
virtualinherited

◆ clearOutputForces()

void PLMD::ActionAtomistic::clearOutputForces ( )
inherited

◆ componentIsNotPeriodic()

void PLMD::ActionWithValue::componentIsNotPeriodic ( const std::string &  name)
inherited

Set your value component to have no periodicity.

◆ componentIsPeriodic()

void PLMD::ActionWithValue::componentIsPeriodic ( const std::string &  name,
const std::string &  min,
const std::string &  max 
)
inherited

Set the value to be periodic with a particular domain.

◆ componentsAreNotOptional()

void PLMD::ActionWithValue::componentsAreNotOptional ( Keywords keys)
staticinherited

Puts a message into the manual that the components always output.

◆ copyOutput() [1/2]

Value * PLMD::ActionWithValue::copyOutput ( const std::string &  name) const
inherited

Return a pointer to the value with name (this is used to retrieve values in other PLMD::Actions) You should NEVER use this routine to refer to the components of your PLMD::Action.

Use getPntrToComponent instead.

◆ copyOutput() [2/2]

Value * PLMD::ActionWithValue::copyOutput ( const unsigned &  n) const
inherited

Return a pointer to the value with this number (this is used to retrieve values in other PLMD::Actions) You should NEVER use this routine to refer to the components of your PLMD::Action.

Use getPntrToComponent instead.

◆ deactivate()

void PLMD::Action::deactivate ( )
inlinevirtualinherited

Set action to inactive.

◆ deactivateAllTasks()

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

Deactivate all the tasks in the task list.

◆ derivativesAreRequired()

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

Are derivatives required for this quantity.

◆ difference()

double PLMD::ActionWithArguments::difference ( int  i,
double  d1,
double  d2 
) const
inlineinherited

Takes the difference taking into account pbc for arg i.

◆ dissimilaritiesWereSet()

bool PLMD::analysis::AnalysisBase::dissimilaritiesWereSet ( ) const
inlinevirtual

◆ doJobsRequiredBeforeTaskList()

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

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

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

◆ doNotCalculateDerivatives()

bool PLMD::ActionWithValue::doNotCalculateDerivatives ( ) const
inlinevirtualinherited

Are we not calculating derivatives.

Reimplemented in PLMD::multicolvar::MultiColvarBase.

◆ doNotForce()

void PLMD::ActionAtomistic::doNotForce ( )
inlineinherited

Skip atom forces - use with care.

If this function is called during initialization, then forces are not going to be propagated. Can be used for optimization.

◆ doNotRetrieve()

void PLMD::ActionAtomistic::doNotRetrieve ( )
inlineinherited

Skip atom retrieval - use with care.

If this function is called during initialization, then atoms are not going to be retrieved. Can be used for optimization. Notice that calling getPosition(int) in an Action where DoNotRetrieve() was called might lead to undefined behavior.

◆ error()

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

Crash calculation and print documentation.

◆ exists()

bool PLMD::ActionWithValue::exists ( const std::string &  name) const
inherited

Check if a value with a particular name is present.

This is only used in PLMD::ActionWithArguments. You should not use it when manipulating components.

◆ exit()

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

Exit with error code c.

◆ expandArgKeywordInPDB()

void PLMD::ActionWithArguments::expandArgKeywordInPDB ( PDB pdb)
protectedinherited

This changes the arg keyword in the pdb file.

◆ 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)
virtualinherited

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)

◆ getAbsoluteIndex()

AtomNumber PLMD::ActionAtomistic::getAbsoluteIndex ( int  i) const
inlineinherited

Get the absolute index of an atom.

◆ getAbsoluteIndexes()

const std::vector< AtomNumber > & PLMD::ActionAtomistic::getAbsoluteIndexes ( ) const
inlinevirtualinherited

Get the vector of absolute indexes.

Reimplemented in PLMD::multicolvar::BridgedMultiColvarFunction.

◆ getActiveTask()

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

Get the ith of the currently active tasks.

◆ getArgument()

double PLMD::ActionWithArguments::getArgument ( const unsigned  n) const
inlineinherited

Returns the value of an argument.

◆ getArgumentList()

std::vector< Value * > PLMD::analysis::AnalysisBase::getArgumentList ( )
inlinevirtual

Overwrite getArguments so we get arguments from underlying class.

Reimplemented in PLMD::analysis::ReadAnalysisFrames, PLMD::dimred::ProjectNonLandmarkPoints, PLMD::dimred::SketchMapRead, and PLMD::dimred::DimensionalityReductionBase.

◆ getArgumentNames()

std::vector< std::string > PLMD::analysis::AnalysisBase::getArgumentNames ( )

Get the list of argument names in the base.

◆ getArguments()

const std::vector< Value * > & PLMD::ActionWithArguments::getArguments ( ) const
inlinevirtualinherited

Returns an array of pointers to the arguments.

◆ getAtomIndexes()

const std::vector< AtomNumber > & PLMD::analysis::AnalysisBase::getAtomIndexes ( ) const
inlinevirtual

Get the indices of the atoms that have been stored.

Reimplemented in PLMD::analysis::ReadAnalysisFrames.

◆ getBox()

const Tensor & PLMD::ActionAtomistic::getBox ( ) const
inlineinherited

Get box shape.

◆ getCharge()

double PLMD::ActionAtomistic::getCharge ( int  i) const
inlineinherited

Get charge of i-th atom.

◆ getComponentsList()

std::string PLMD::ActionWithValue::getComponentsList ( ) const
inherited

get a string that contains all the available components

◆ getComponentsVector()

std::vector< std::string > PLMD::ActionWithValue::getComponentsVector ( ) const
inherited

get a vector that contains the label for all the components

◆ getCPT()

bool PLMD::Action::getCPT ( ) const
inherited

Return true if we are doing at a checkpoint step.

◆ getCurrentNumberOfActiveTasks()

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

Get the number of tasks that are currently active.

◆ getDataPointIndexInBase()

unsigned PLMD::analysis::AnalysisBase::getDataPointIndexInBase ( const unsigned &  idata) const
inlinevirtual

◆ getDependencies()

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

Return dependencies.

◆ getDissimilarity()

double PLMD::analysis::AnalysisBase::getDissimilarity ( const unsigned &  i,
const unsigned &  j 
)
inlinevirtual

Get the squared dissimilarity between two reference configurations.

Reimplemented in PLMD::analysis::ReadDissimilarityMatrix, PLMD::dimred::SketchMapRead, PLMD::analysis::LandmarkSelectionBase, and PLMD::analysis::EuclideanDissimilarityMatrix.

◆ getDissimilarityInstruction()

std::string PLMD::analysis::AnalysisBase::getDissimilarityInstruction ( ) const
inlinevirtual

Get the information on how dissimilarities were calculated for output PDB.

Reimplemented in PLMD::analysis::ReadAnalysisFrames, and PLMD::analysis::EuclideanDissimilarityMatrix.

◆ getDocumentation()

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

◆ getEnergy()

const double & PLMD::ActionAtomistic::getEnergy ( ) const
inlineinherited

Get energy.

◆ 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)
protectedinherited

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

◆ getFullNumberOfTasks()

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

Get the full size of the taskList dynamic list.

◆ getGlobalPosition()

const Vector & PLMD::ActionAtomistic::getGlobalPosition ( AtomNumber  i) const
inlineinherited

Get position of i-th atom (access by absolute AtomNumber).

With direct access to the global atom array.

Warning
Should be only used by actions that need to read the shared position array. This array is insensitive to local changes such as makeWhole(), numerical derivatives, etc.

◆ 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.

◆ getMass()

double PLMD::ActionAtomistic::getMass ( int  i) const
inlineinherited

Get mass of i-th atom.

◆ getMetricName()

std::string PLMD::analysis::AnalysisBase::getMetricName ( ) const
inlinevirtual

Get the name of the metric that is being used.

◆ getName()

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

Returns the name.

◆ getNLTolerance()

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

Return the value for the neighbor list tolerance.

◆ getNormalization()

double PLMD::analysis::AnalysisBase::getNormalization ( ) const
inlinevirtual

Return the normalisation constant for the calculation.

◆ getNumberOfArguments()

unsigned PLMD::ActionWithArguments::getNumberOfArguments ( ) const
inlinevirtualinherited

Returns the number of arguments.

Reimplemented in PLMD::vesselbase::ActionWithAveraging.

◆ getNumberOfAtoms()

unsigned PLMD::ActionAtomistic::getNumberOfAtoms ( ) const
inlineinherited

Get number of available atoms.

◆ getNumberOfComponents()

int PLMD::ActionWithValue::getNumberOfComponents ( ) const
inlineinherited

Returns the number of values defined.

◆ getNumberOfDataPoints()

unsigned PLMD::analysis::AnalysisBase::getNumberOfDataPoints ( ) const
inlinevirtual

◆ getNumberOfDerivatives()

unsigned PLMD::analysis::AnalysisBase::getNumberOfDerivatives ( )
inlineoverridevirtual

Implements PLMD::ActionWithValue.

◆ getNumberOfQuantities()

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

◆ getNumberOfVessels()

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

Get the number of vessels.

◆ getOutputQuantity() [1/2]

double PLMD::ActionWithValue::getOutputQuantity ( const unsigned  j) const
inlineinherited

Get the value of one of the components of the PLMD::Action.

◆ getOutputQuantity() [2/2]

double PLMD::ActionWithValue::getOutputQuantity ( const std::string &  name) const
inlineinherited

Get the value with a specific name (N.B. if there is no such value this returns zero)

◆ getPbc()

const Pbc & PLMD::ActionAtomistic::getPbc ( ) const
inlineinherited

Get reference to Pbc.

◆ getPntrToArgument()

Value * PLMD::ActionWithArguments::getPntrToArgument ( const unsigned  n)
inlineinherited

Return a pointer to specific argument.

◆ getPntrToComponent() [1/2]

Value * PLMD::ActionWithValue::getPntrToComponent ( int  i)
protectedinherited

Return a pointer to the component by index.

◆ getPntrToComponent() [2/2]

Value * PLMD::ActionWithValue::getPntrToComponent ( const std::string &  name)
protectedinherited

Return a pointer to the value by name.

◆ getPntrToValue()

Value * PLMD::ActionWithValue::getPntrToValue ( )
protectedinherited

Get a pointer to the default value.

◆ getPntrToVessel()

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

Get a pointer to the ith vessel.

◆ getPosition()

const Vector & PLMD::ActionAtomistic::getPosition ( int  i) const
inlineinherited

Get position of i-th atom (access by relative index)

◆ getPositionInCurrentTaskList()

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

Return the position in the current task list.

◆ getPositionInFullTaskList()

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

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

◆ getPositions()

const std::vector< Vector > & PLMD::ActionAtomistic::getPositions ( ) const
inlineinherited

Get the array of all positions.

◆ getProjection()

double PLMD::ActionWithArguments::getProjection ( unsigned  i,
unsigned  j 
) const
inherited

Get the scalar product between the gradients of two variables.

◆ getRestart()

bool PLMD::Action::getRestart ( ) const
inlineinherited

Return true if we are doing a restart.

◆ getSizeOfBuffer()

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

Get the size of the buffer.

◆ getStep()

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

Return the present timestep.

◆ getStoredData()

DataCollectionObject & PLMD::analysis::AnalysisBase::getStoredData ( const unsigned &  idata,
const bool &  calcdist 
)
inlinevirtual

Get a reference configuration (in dimensionality reduction this returns the projection)

Reimplemented in PLMD::analysis::ReadAnalysisFrames, PLMD::analysis::ReadDissimilarityMatrix, PLMD::dimred::ProjectNonLandmarkPoints, PLMD::dimred::SketchMapRead, and PLMD::analysis::LandmarkSelectionBase.

◆ getStride()

int PLMD::ActionPilot::getStride ( ) const
inherited

Get the stride.

◆ getTaskCode()

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

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
inlineprotectedinherited

Return the value of the tolerance.

◆ getTotAtoms()

unsigned PLMD::ActionAtomistic::getTotAtoms ( ) const
inlineinherited

Get total number of atoms, including virtual ones.

Can be used to make a loop on modifyGlobalPosition or getGlobalPosition.

◆ getUnique()

const std::set< AtomNumber > & PLMD::ActionAtomistic::getUnique ( ) const
inlineinherited

◆ getUniqueLocal()

const std::set< AtomNumber > & PLMD::ActionAtomistic::getUniqueLocal ( ) const
inlineinherited

◆ getVesselWithName()

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

These are overwritten in MultiColvarFunction.

Return a particular named vessel

◆ getWeight()

double PLMD::analysis::AnalysisBase::getWeight ( const unsigned &  idata)
inlinevirtual

◆ interpretArgumentList()

void PLMD::ActionWithArguments::interpretArgumentList ( const std::vector< std::string > &  c,
std::vector< Value *> &  arg 
)
inherited

Convert a list of argument names into a list of pointers to the values.

◆ interpretAtomList()

void PLMD::ActionAtomistic::interpretAtomList ( std::vector< std::string > &  strings,
std::vector< AtomNumber > &  t 
)
inherited

Convert a set of read in strings into an atom list (this is used in parseAtomList)

◆ 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()

bool PLMD::analysis::AnalysisBase::isPeriodic ( )
inlineoverridevirtual

These overwrite things from inherited classes (this is a bit of a fudge)

Implements PLMD::vesselbase::ActionWithVessel.

◆ lockContributors()

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

◆ lockRequests()

void PLMD::analysis::AnalysisBase::lockRequests ( )
inlineoverridevirtual

These are required because we inherit from both ActionAtomistic and ActionWithArguments.

Reimplemented from PLMD::Action.

◆ makeWhole()

void PLMD::ActionAtomistic::makeWhole ( )
inherited

Make atoms whole, assuming they are in the proper order.

◆ modifyForceOnEnergy()

double & PLMD::ActionAtomistic::modifyForceOnEnergy ( )
inlineinherited

Get a reference to force on energy.

◆ modifyForceOnExtraCV()

double & PLMD::ActionAtomistic::modifyForceOnExtraCV ( )
inlineinherited

Get a reference to force on extraCV.

◆ modifyForces()

std::vector< Vector > & PLMD::ActionAtomistic::modifyForces ( )
inlineinherited

Get a reference to forces array.

◆ modifyGlobalForce()

Vector & PLMD::ActionAtomistic::modifyGlobalForce ( AtomNumber  i)
inlineinherited

Get modifiable force of i-th atom (access by absolute AtomNumber).

Warning
Should be used by action that need to modify the stored atomic forces. This should be used with great care since the plumed core does not usually keep all these forces up to date. In particular, if an action require this, one should during constructor call allowToAccessGlobalForces(). Notice that for efficiency reason plumed does not check if this is done!

◆ modifyGlobalPbc()

Pbc & PLMD::ActionAtomistic::modifyGlobalPbc ( )
inlineinherited

Get modifiable PBC Should be used by action that need to modify the stored box.

◆ modifyGlobalPosition()

Vector & PLMD::ActionAtomistic::modifyGlobalPosition ( AtomNumber  i)
inlineinherited

Get modifiable position of i-th atom (access by absolute AtomNumber).

Warning
Should be only used by actions that need to modify the shared position array. This array is insensitive to local changes such as makeWhole(), numerical derivatives, etc.

◆ modifyGlobalVirial()

Tensor & PLMD::ActionAtomistic::modifyGlobalVirial ( )
inlineinherited

Get modifiable virial Should be used by action that need to modify the stored virial.

◆ modifyVirial()

Tensor & PLMD::ActionAtomistic::modifyVirial ( )
inlineinherited

Get a reference to virial array.

◆ needsDerivatives()

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

Turn on the derivatives in the vessel.

◆ noAnalyticalDerivatives()

void PLMD::ActionWithValue::noAnalyticalDerivatives ( Keywords keys)
staticinherited

Insist that numerical derivatives should always be used for an action and make this fact appear in the manual.

◆ normalizeVector()

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

◆ normalizeVectorDerivatives()

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

◆ onStep()

bool PLMD::ActionPilot::onStep ( ) const
virtualinherited

Check if the action is active on this step.

Reimplemented in PLMD::gridtools::ConvertToFES.

◆ parse()

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

Parse one keyword as generic type.

◆ parseArgumentList() [1/2]

void PLMD::ActionWithArguments::parseArgumentList ( const std::string &  key,
std::vector< Value *> &  args 
)
inherited

Parse a list of arguments.

◆ parseArgumentList() [2/2]

bool PLMD::ActionWithArguments::parseArgumentList ( const std::string &  key,
int  i,
std::vector< Value *> &  args 
)
inherited

Parse a numbered list of arguments.

◆ parseAtomList() [1/2]

void PLMD::ActionAtomistic::parseAtomList ( const std::string &  key,
std::vector< AtomNumber > &  t 
)
inherited

Parse a list of atoms without a numbered keyword.

◆ parseAtomList() [2/2]

void PLMD::ActionAtomistic::parseAtomList ( const std::string &  key,
const int  num,
std::vector< AtomNumber > &  t 
)
inherited

Parse an list of atom with a numbred keyword.

◆ 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.

◆ pbcApply()

void PLMD::ActionAtomistic::pbcApply ( std::vector< Vector > &  dlist,
unsigned  max_index = 0 
) const
inherited

Applies PBCs to a seriens of positions or distances.

◆ pbcDistance()

Vector PLMD::ActionAtomistic::pbcDistance ( const Vector v1,
const Vector v2 
) const
inherited

Compute the pbc distance between two positions.

◆ performAnalysis()

virtual void PLMD::analysis::AnalysisBase::performAnalysis ( )
pure virtual

◆ performTask()

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

◆ 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::gridtools::ConvertToFES, PLMD::SetupMolInfo, PLMD::colvar::Energy, PLMD::colvar::ExtraCV, and PLMD::colvar::CoordinationBase.

◆ readAtomsFromPDB() [1/2]

void PLMD::ActionAtomistic::readAtomsFromPDB ( const PDB pdb)
overridevirtualinherited

Read in an input file containing atom positions and calculate the action for the atomic configuration therin.

Reimplemented from PLMD::Action.

◆ readAtomsFromPDB() [2/2]

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 ( )
protectedinherited

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

◆ registerKeywords()

void PLMD::analysis::AnalysisBase::registerKeywords ( Keywords keys)
static

◆ requestArguments()

void PLMD::ActionWithArguments::requestArguments ( const std::vector< Value *> &  arg)
inherited

Setup the dependencies.

◆ requestAtoms()

void PLMD::ActionAtomistic::requestAtoms ( const std::vector< AtomNumber > &  a,
const bool  clearDep = true 
)
inherited

Request an array of atoms.

This method is used to ask for a list of atoms. Atoms should be asked for by number. If this routine is called during the simulation, atoms will be available at the next step MAYBE WE HAVE TO FIND SOMETHING MORE CLEAR FOR DYNAMIC LISTS OF ATOMS

◆ resizeFunctions()

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

Resize all the functions when the number of derivatives change.

◆ retrieveAtoms()

void PLMD::ActionAtomistic::retrieveAtoms ( )
virtualinherited

◆ retrieveDomain()

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

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 ( )
protectedinherited

Calculate the values of all the vessels.

◆ runFinalJobs()

void PLMD::analysis::AnalysisBase::runFinalJobs ( )
overridevirtual

This calls the analysis to be performed in the final step of the calculation i.e.

when use_all_data is true

Reimplemented from PLMD::Action.

Reimplemented in PLMD::analysis::ReadDissimilarityMatrix.

◆ serialCalculation()

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

Is the calculation being done in serial.

◆ setExtraCV()

void PLMD::ActionAtomistic::setExtraCV ( const std::string &  name)
inlineprotectedinherited

◆ setForcesOnAtoms()

void PLMD::ActionAtomistic::setForcesOnAtoms ( const std::vector< double > &  forcesToApply,
unsigned  ind = 0 
)
inherited

Add the forces to the atoms.

◆ setGradientsIfNeeded()

void PLMD::ActionWithValue::setGradientsIfNeeded ( )
inherited

Calculate the gradients and store them for all the values (need for projections)

◆ setLowMemOption()

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

Set that we are using low memory.

◆ setNotPeriodic()

void PLMD::ActionWithValue::setNotPeriodic ( )
inherited

Set your default value to have no periodicity.

◆ setOption()

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

◆ setPeriodic()

void PLMD::ActionWithValue::setPeriodic ( const std::string &  min,
const std::string &  max 
)
inherited

Set the value to be periodic with a particular domain.

◆ setStride()

void PLMD::ActionPilot::setStride ( const int &  n)
inherited

Set the value of the stride.

◆ setValue() [1/2]

void PLMD::ActionWithValue::setValue ( const double &  d)
inlineprotectedinherited

Set the default value (the one without name)

◆ setValue() [2/2]

void PLMD::ActionWithValue::setValue ( Value ,
double   
)
inherited

Set the value.

◆ taskIsCurrentlyActive()

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

Check whether or not a particular task is currently active.

◆ threadSafe()

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

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
virtualinherited

Do the task if we have a bridge.

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

◆ turnOnDerivatives()

void PLMD::ActionWithValue::turnOnDerivatives ( )
virtualinherited

◆ unlockRequests()

void PLMD::analysis::AnalysisBase::unlockRequests ( )
inlineoverridevirtual

Reimplemented from PLMD::Action.

◆ update()

void PLMD::analysis::AnalysisBase::update ( )
overridevirtual

This will call the analysis to be performed.

Reimplemented from PLMD::Action.

Reimplemented in PLMD::analysis::ReadDissimilarityMatrix, and PLMD::analysis::ReadAnalysisFrames.

◆ updateUniqueLocal()

void PLMD::ActionAtomistic::updateUniqueLocal ( )
inherited

updates local unique atoms

◆ useCustomisableComponents()

void PLMD::ActionWithValue::useCustomisableComponents ( Keywords keys)
staticinherited

The components in the action will depend on the user.

◆ useNumericalDerivatives()

void PLMD::ActionWithValue::useNumericalDerivatives ( )
inlineinherited

This forces the class to use numerical derivatives.

◆ usingLowMem()

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

Are we using low memory.

◆ usingMemory()

bool PLMD::analysis::AnalysisBase::usingMemory ( ) const
inlinevirtual

Are we using memory in this calculation this affects the weights of points.

◆ warning()

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

Issue a warning.

◆ weightWithDerivatives()

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

Does the weight have derivatives.

Friends And Related Function Documentation

◆ ReadDissimilarityMatrix

friend class ReadDissimilarityMatrix
friend

◆ ReselectLandmarks

friend class ReselectLandmarks
friend

Member Data Documentation

◆ atoms

Atoms& PLMD::ActionAtomistic::atoms
protectedinherited

◆ bridgeVariable

unsigned PLMD::vesselbase::ActionWithVessel::bridgeVariable
protectedinherited

This is used for numerical derivatives of bridge variables.

◆ comm

Communicator& PLMD::Action::comm
inherited

◆ contributorsAreUnlocked

bool PLMD::vesselbase::ActionWithVessel::contributorsAreUnlocked
protectedinherited

The terms in the series are locked.

◆ dertime

bool PLMD::vesselbase::ActionWithVessel::dertime
protectedinherited

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

◆ files

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

◆ keywords

const Keywords& PLMD::Action::keywords
inherited

◆ log

Log& PLMD::Action::log
inherited

Reference to the log stream.

◆ multi_sim_comm

Communicator& PLMD::Action::multi_sim_comm
inherited

◆ my_input_data

AnalysisBase* PLMD::analysis::AnalysisBase::my_input_data
protected

The Analysis action that we are reusing data from.

◆ mydata

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

A pointer to the object that stores data.

◆ plumed

PlumedMain& PLMD::Action::plumed
inherited

Reference to main plumed object.

◆ taskFlags

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

This list is used to update the neighbor list.

◆ weightHasDerivatives

bool PLMD::vesselbase::ActionWithVessel::weightHasDerivatives
protectedinherited

Does the weight have derivatives.


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