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


This is the abstract base class to use for implementing new methods for analyzing the trajectory, within it there is information as to how to go about implementing a new analysis method. More...

#include <Analysis.h>

Inheritance diagram for PLMD::analysis::Analysis:
Inheritance graph
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Public Types

typedef std::vector< Action * > Dependencies
 

Public Member Functions

 Analysis (const ActionOptions &)
 
 ~Analysis ()
 
void calculate ()
 Calculate an Action. More...
 
void apply ()
 Apply an Action. More...
 
void accumulate ()
 
void performOperations (const bool &from_update)
 This does the averaging operation. More...
 
virtual void performAnalysis ()=0
 
void runFinalJobs ()
 RunFinalJobs This method is called once at the very end of the calculation. More...
 
void runAnalysis ()
 
bool isPeriodic ()
 Are the base quantities periodic. More...
 
virtual void finalizeWeights (const bool &ignore_weights)
 Convert the stored log weights to proper weights. More...
 
void lockRequests ()
 
void unlockRequests ()
 
void calculateNumericalDerivatives (PLMD::ActionWithValue *)
 N.B. More...
 
virtual unsigned getNumberOfDerivatives ()
 
unsigned getNumberOfArguments () const
 Returns the number of arguments. More...
 
std::vector< Value * > getArguments ()
 Overwrite ActionWithArguments getArguments() so that we don't return the bias. More...
 
const std::vector< Value * > & getArguments () const
 Returns an array of pointers to the arguments. More...
 
void update ()
 Update. More...
 
virtual void clearAverage ()
 This does the clearing of the action. More...
 
virtual void prepareForAveraging ()
 This is done before the averaging comences. More...
 
virtual void finishAveraging ()
 This is done once the averaging is finished. More...
 
virtual bool onStep () const
 Check if the action is active on this step. More...
 
void setStride (const int &n)
 Set the value of the stride. More...
 
int getStride () const
 Get the stride. More...
 
bool checkUpdate () const
 Check if action should be updated. More...
 
void addDependency (Action *)
 Specify that this Action depends on another one. More...
 
void clearDependencies ()
 Clear the dependence list for this Action. More...
 
long int getStep () const
 Return the present timestep. More...
 
double getTime () const
 Return the present time. More...
 
double getTimeStep () const
 Return the timestep. More...
 
bool getRestart () const
 Return true if we are doing a restart. More...
 
bool getCPT () const
 Return true if we are doing at a checkpoint step. More...
 
std::string getKeyword (const std::string &key)
 Just read one of the keywords and return the whole thing as a string. More...
 
template<class T >
void parse (const std::string &key, T &t)
 Parse one keyword as generic type. 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 >
void parseVector (const std::string &key, std::vector< T > &t)
 Parse one keyword as std::vector. More...
 
template<class T >
bool parseNumberedVector (const std::string &key, const int no, std::vector< T > &t)
 Parse a vector with a number. More...
 
void parseFlag (const std::string &key, bool &t)
 Parse one keyword as boolean flag. More...
 
void error (const std::string &msg) const
 Crash calculation and print documentation. More...
 
void warning (const std::string &msg)
 Issue a warning. More...
 
void exit (int c=0)
 Exit with error code c. More...
 
void checkRead ()
 Check if Action was properly read. 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 beforeUpdate ()
 Before Update. More...
 
void fflush ()
 Tell to the Action to flush open files. More...
 
virtual std::string getDocumentation () const
 
const std::string & getLabel () const
 Returns the label. More...
 
const std::string & getName () const
 Returns the name. More...
 
virtual void activate ()
 Set action to active. More...
 
virtual void setOption (const std::string &s)
 
virtual void clearOptions ()
 
virtual void deactivate ()
 Set action to inactive. More...
 
bool isActive () const
 Check if action is active. More...
 
bool isOptionOn (const std::string &s) const
 Check if an option is on. More...
 
const DependenciesgetDependencies () const
 Return dependencies. More...
 
virtual bool checkNumericalDerivatives () const
 Check if numerical derivatives should be performed. More...
 
bool checkNumericalDerivatives () const
 Check if numerical derivatives should be used. More...
 
virtual bool checkNeedsGradients () const
 Check if the action needs gradient. More...
 
FILE * fopen (const char *path, const char *mode)
 Opens a file. More...
 
int fclose (FILE *fp)
 Closes a file opened with Action::fclose(). More...
 
void calculateFromPDB (const PDB &)
 Calculate the action given a pdb file as input. 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 readAtomsFromPDB (const PDB &pdb)
 Read in an input file containing atom positions and calculate the action for the atomic configuration therin. More...
 
bool getExchangeStep () const
 Check if we are on an exchange step. More...
 
std::string cite (const std::string &s)
 Cite a paper see PlumedMain::cite. More...
 
void requestAtoms (const std::vector< AtomNumber > &a)
 Request an array of atoms. More...
 
const VectorgetPosition (int) const
 Get position of i-th atom (access by relative index) More...
 
const VectorgetPosition (AtomNumber) const
 Get position of i-th atom (access by absolute AtomNumber). More...
 
VectormodifyPosition (AtomNumber)
 Get modifiable position of i-th atom (access by absolute AtomNumber). More...
 
unsigned getTotAtoms () const
 Get total number of atoms, including virtual ones. More...
 
VectormodifyGlobalForce (AtomNumber)
 Get modifiable force 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...
 
PbcmodifyGlobalPbc ()
 Get modifiable PBC Should be used by action that need to modify the stored box. More...
 
const TensorgetBox () const
 Get box shape. More...
 
const std::vector< Vector > & getPositions () const
 Get the array of all positions. More...
 
const double & getEnergy () const
 Get energy. More...
 
double getMass (int i) const
 Get mass of i-th atom. More...
 
double getCharge (int i) const
 Get charge of i-th atom. More...
 
std::vector< Vector > & modifyForces ()
 Get a reference to forces array. More...
 
TensormodifyVirial ()
 Get a reference to virial array. More...
 
double & modifyForceOnEnergy ()
 Get a reference to force on energy. More...
 
unsigned getNumberOfAtoms () const
 Get number of available atoms. More...
 
Vector pbcDistance (const Vector &, const Vector &) const
 Compute the pbc distance between two positions. More...
 
void pbcApply (std::vector< Vector > &dlist, unsigned max_index=0) const
 Applies PBCs to a seriens of positions or distances. More...
 
virtual const std::vector< AtomNumber > & getAbsoluteIndexes () const
 Get the vector of absolute indexes. More...
 
AtomNumber getAbsoluteIndex (int i) const
 Get the absolute index of an atom. 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 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...
 
void changeBox (const Tensor &newbox)
 Change the box shape. More...
 
const PbcgetPbc () const
 Get reference to Pbc. More...
 
void setForcesOnAtoms (const std::vector< double > &forcesToApply, unsigned ind=0)
 Add the forces to the atoms. More...
 
void doNotRetrieve ()
 Skip atom retrieval - use with care. More...
 
void doNotForce ()
 Skip atom forces - use with care. More...
 
void makeWhole ()
 Make atoms whole, assuming they are in the proper order. More...
 
void allowToAccessGlobalForces ()
 Allow calls to modifyGlobalForce() More...
 
void updateUniqueLocal ()
 updates local unique atoms More...
 
void clearOutputForces ()
 
void calculateAtomicNumericalDerivatives (ActionWithValue *a, const unsigned &startnum)
 Numerical derivative routine to use when using Actions that inherit from BOTH ActionWithArguments and ActionAtomistic. More...
 
virtual void retrieveAtoms ()
 
void applyForces ()
 
const std::set< AtomNumber > & getUnique () const
 
const std::set< AtomNumber > & getUniqueLocal () const
 
double getProjection (unsigned i, unsigned j) const
 Get the scalar product between the gradients of two variables. More...
 
double getArgument (const unsigned n) const
 Returns the value of an argument. More...
 
ValuegetPntrToArgument (const unsigned n)
 Return a pointer to specific argument. More...
 
double difference (int, double, double) const
 Takes the difference taking into account pbc for arg i. More...
 
double bringBackInPbc (int i, double d1) const
 Takes one value and brings it back into the pbc of argument i. 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 requestArguments (const std::vector< Value *> &arg)
 Setup the dependencies. More...
 
void addForcesOnArguments (const std::vector< double > &forces)
 Add forces to arguments (used in apply) 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 addValue ()
 Add a value with the name label. More...
 
void addValueWithDerivatives ()
 Add a value with the name label that has derivatives. More...
 
void setNotPeriodic ()
 Set your default value to have no periodicity. More...
 
void setPeriodic (const std::string &min, const std::string &max)
 Set the value to be periodic with a particular domain. More...
 
void setValue (Value *, double)
 Set the value. 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 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...
 
virtual bool doNotCalculateDerivatives () const
 Are we not calculating derivatives. 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...
 
bool exists (const std::string &name) const
 Check if a value with a particular name is present. 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...
 
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...
 
int getNumberOfComponents () const
 Returns the number of values defined. More...
 
void clearInputForces ()
 Clear the forces on the values. More...
 
virtual void clearDerivatives ()
 Clear the derivatives of values wrt parameters. More...
 
void setGradientsIfNeeded ()
 Calculate the gradients and store them for all the values (need for projections) More...
 
void useNumericalDerivatives ()
 This forces the class to use numerical derivatives. More...
 
virtual void checkFieldsAllowed ()
 
virtual void turnOnDerivatives ()
 Activate the calculation of derivatives. More...
 
void lockContributors ()
 
unsigned getCurrentNumberOfActiveTasks () const
 Get the number of tasks that are currently active. More...
 
bool taskIsCurrentlyActive (const unsigned &index) const
 Check whether or not a particular task is currently active. More...
 
bool derivativesAreRequired () const
 Are derivatives required for this quantity. More...
 
virtual bool threadSafe () const
 Is this action thread safe. More...
 
virtual void finishComputations (const std::vector< double > &buffer)
 Finish running all the calculations. More...
 
virtual void retrieveDomain (std::string &min, std::string &max)
 What are the domains of the base quantities. 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...
 
virtual void doJobsRequiredBeforeTaskList ()
 Do any jobs that are required before the task list is undertaken. More...
 
unsigned getFullNumberOfTasks () const
 Get the full size of the taskList dynamic list. More...
 
unsigned getPositionInFullTaskList (const unsigned &ii) const
 Get the position of the ith active task in the full list. More...
 
unsigned getTaskCode (const unsigned &ii) const
 Get the code for the ii th task in the list. More...
 
unsigned getActiveTask (const unsigned &ii) const
 Get the ith of the currently active tasks. More...
 
virtual void performTask (const unsigned &, const unsigned &, MultiValue &) const =0
 Calculate one of the functions in the distribution. More...
 
virtual void transformBridgedDerivatives (const unsigned &current, MultiValue &invals, MultiValue &outvals) const
 Do the task if we have a bridge. More...
 
StoreDataVesselbuildDataStashes (ActionWithVessel *actionThatUses)
 Ensure that data required in other vessels is stored. More...
 
virtual void applyBridgeForces (const std::vector< double > &bb)
 Apply forces from bridge vessel - this is rarely used - currently only in ActionVolume. More...
 
VesselgetVesselWithName (const std::string &mynam)
 These are overwritten in MultiColvarFunction. More...
 
bool weightWithDerivatives () const
 Does the weight have derivatives. More...
 
unsigned getPositionInCurrentTaskList (const unsigned &myind) const
 Return the position in the current task list. More...
 
virtual void normalizeVector (std::vector< double > &vals) const
 These normalizes vectors and is used in StoreDataVessel. More...
 
virtual void normalizeVectorDerivatives (MultiValue &myvals) const
 

Static Public Member Functions

static void registerKeywords (Keywords &keys)
 Finalize the weights without using the log sums. 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 componentsAreNotOptional (Keywords &keys)
 Puts a message into the manual that the components always output. More...
 
static void useCustomisableComponents (Keywords &keys)
 The components in the action will depend on the user. More...
 

Public Attributes

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

Protected Member Functions

void parseOutputFile (const std::string &key, std::string &filename)
 This is used to read in output file names for analysis methods. More...
 
std::string getMetricName () const
 Get the name of the metric we are using to measure distances. More...
 
unsigned getNumberOfDataPoints () const
 Return the number of data points. More...
 
double getWeight (const unsigned &idata) const
 Return the weight of the ith point. More...
 
void getDataPoint (const unsigned &idata, std::vector< double > &point, double &weight) const
 Retrieve the ith point. More...
 
bool getPeriodicityInformation (const unsigned &i, std::string &dmin, std::string &dmax)
 Returns true if argument i is periodic together with the domain. More...
 
bool usingMemory () const
 Are we analyzing each data block separately (if we are not this also returns the old normalization ) More...
 
std::string getOutputFormat () const
 Return the format to use for numbers in output files. More...
 
void setAveragingAction (AveragingVessel *av_vessel, const bool &usetasks)
 Set the averaging action. More...
 
bool noNormalization () const
 Check if we are using the normalization condition when calculating this quantity. More...
 
void expandArgKeywordInPDB (PDB &pdb)
 This changes the arg keyword in the pdb file. More...
 
ValuegetPntrToValue ()
 Get a pointer to the default value. More...
 
void setValue (const double &d)
 Set the default value (the one without name) 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...
 
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 (Vessel *vv)
 
BridgeVesseladdBridgingVessel (ActionWithVessel *tome)
 Add a bridging vessel to the list of vessels. More...
 
void readVesselKeywords ()
 Complete the setup of this object (this routine must be called after construction of ActionWithValue) More...
 
void needsDerivatives ()
 Turn on the derivatives in the vessel. More...
 
double getTolerance () const
 Return the value of the tolerance. More...
 
double getNLTolerance () const
 Return the value for the neighbor list tolerance. More...
 
void runAllTasks ()
 Calculate the values of all the vessels. More...
 
void resizeFunctions ()
 Resize all the functions when the number of derivatives change. More...
 
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...
 
bool getForcesFromVessels (std::vector< double > &forcesToApply)
 Retrieve the forces from all the vessels (used in apply) More...
 
bool serialCalculation () const
 Is the calculation being done in serial. More...
 
bool usingLowMem () const
 Are we using low memory. More...
 
void setLowMemOption (const bool &)
 Set that we are using low memory. More...
 
void deactivateAllTasks ()
 Deactivate all the tasks in the task list. More...
 
unsigned getSizeOfBuffer (unsigned &bufsize)
 Get the size of the buffer. More...
 
void addTaskToList (const unsigned &taskCode)
 Add a task to the full list. More...
 

Protected Attributes

std::vector< std::string > argument_names
 List of argument names. More...
 
std::vector< ReferenceConfiguration * > data
 The data we are going to analyze. More...
 
bool useRunAllTasks
 This ensures runAllTasks is used. More...
 
unsigned clearstride
 The frequency with which to clear the grid. More...
 
double lweight
 The current weight and its logarithm. More...
 
double cweight
 
Atomsatoms
 
bool dertime
 This is also used to minimise computational expense in complex functions. More...
 
bool contributorsAreUnlocked
 The terms in the series are locked. More...
 
bool weightHasDerivatives
 Does the weight have derivatives. More...
 
unsigned bridgeVariable
 This is used for numerical derivatives of bridge variables. 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...
 

Private Member Functions

void readDataFromFile (const std::string &filename)
 Read in data from a file. More...
 
std::vector< double > getMetric () const
 Get the metric if we are using malonobius distance and flexible hill. More...
 

Private Attributes

bool nomemory
 Are we treating each block of data separately. More...
 
bool write_chq
 Are we writing a checkpoint file. More...
 
bool reusing_data
 Are we reusing data stored by another analysis action. More...
 
bool ignore_reweight
 If we are reusing data are we ignoring the reweighting in that data. More...
 
Analysismydatastash
 The Analysis action that we are reusing data from. More...
 
unsigned freq
 The frequency with which we are performing analysis. More...
 
unsigned ndata
 Number of data point we need to run analysis. More...
 
double simtemp
 The temperature at which we are running the calculation. More...
 
double rtemp
 The temperature at which we want the histogram. More...
 
bool needeng
 Do we need the energy (are we reweighting at a different temperature) More...
 
unsigned idata
 The piece of data we are inserting. More...
 
std::vector< double > logweights
 The weights of all the data points. More...
 
std::string ofmt
 Have we analyzed the data for the first time. More...
 
std::vector< double > current_args
 Tempory vector to store values of arguments. More...
 
std::string metricname
 The type of metric we are using to measure distances. More...
 
OFile rfile
 The checkpoint file. More...
 

Detailed Description


This is the abstract base class to use for implementing new methods for analyzing the trajectory, within it there is information as to how to go about implementing a new analysis method.

Member Typedef Documentation

◆ Dependencies

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

Constructor & Destructor Documentation

◆ Analysis()

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

◆ ~Analysis()

PLMD::analysis::Analysis::~Analysis ( )

Member Function Documentation

◆ accumulate()

void PLMD::analysis::Analysis::accumulate ( )

◆ 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 ( Vessel vv)
protectedinherited

◆ allowToAccessGlobalForces()

void PLMD::ActionAtomistic::allowToAccessGlobalForces ( )
inlineinherited

Allow calls to modifyGlobalForce()

◆ apply()

void PLMD::analysis::Analysis::apply ( )
inlinevirtual

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::Analysis::calculate ( )
inlinevirtual

Calculate an Action.

This method is called one or more times per step. The set of all Actions is calculated in forward order.

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::vesselbase::ActionWithAveraging::calculateNumericalDerivatives ( PLMD::ActionWithValue a)
virtualinherited

N.B.

only pass an ActionWithValue to this routine if you know exactly what you are doing. The default will be correct for the vast majority of cases

Reimplemented from PLMD::ActionAtomistic.

◆ changeBox()

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

Change the box shape.

◆ checkFieldsAllowed()

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

Reimplemented in 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
inlinevirtualinherited

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.

◆ clearAverage()

void PLMD::vesselbase::ActionWithAveraging::clearAverage ( )
virtualinherited

◆ 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.

◆ 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.

◆ finalizeWeights()

void PLMD::analysis::Analysis::finalizeWeights ( const bool &  ignore_weights)
virtual

Convert the stored log weights to proper weights.

◆ finishAveraging()

virtual void PLMD::vesselbase::ActionWithAveraging::finishAveraging ( )
inlinevirtualinherited

This is done once the averaging is finished.

Reimplemented in PLMD::analysis::Histogram, PLMD::gridtools::FindContour, PLMD::gridtools::FindContourSurface, and PLMD::analysis::Average.

◆ 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.

◆ getArguments() [1/2]

std::vector< Value * > PLMD::vesselbase::ActionWithAveraging::getArguments ( )
inlineinherited

Overwrite ActionWithArguments getArguments() so that we don't return the bias.

◆ getArguments() [2/2]

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

Returns an array of pointers to the arguments.

◆ 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.

◆ getDataPoint()

void PLMD::analysis::Analysis::getDataPoint ( const unsigned &  idata,
std::vector< double > &  point,
double &  weight 
) const
protected

Retrieve the ith point.

◆ getDependencies()

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

Return dependencies.

◆ 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.

◆ 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.

◆ getMetric()

std::vector< double > PLMD::analysis::Analysis::getMetric ( ) const
private

Get the metric if we are using malonobius distance and flexible hill.

◆ getMetricName()

std::string PLMD::analysis::Analysis::getMetricName ( ) const
inlineprotected

Get the name of the metric we are using to measure distances.

◆ 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.

◆ getNumberOfArguments()

unsigned PLMD::vesselbase::ActionWithAveraging::getNumberOfArguments ( ) const
inlinevirtualinherited

Returns the number of arguments.

Reimplemented from PLMD::ActionWithArguments.

◆ 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::Analysis::getNumberOfDataPoints ( ) const
inlineprotected

Return the number of data points.

◆ getNumberOfDerivatives()

virtual unsigned PLMD::vesselbase::ActionWithAveraging::getNumberOfDerivatives ( )
inlinevirtualinherited

◆ getNumberOfQuantities()

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

◆ getNumberOfVessels()

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

Get the number of vessels.

◆ getOutputFormat()

std::string PLMD::analysis::Analysis::getOutputFormat ( ) const
inlineprotected

Return the format to use for numbers in output files.

◆ 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.

◆ getPeriodicityInformation()

bool PLMD::analysis::Analysis::getPeriodicityInformation ( const unsigned &  i,
std::string &  dmin,
std::string &  dmax 
)
protected

Returns true if argument i is periodic together with the domain.

◆ 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() [1/2]

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

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

◆ getPosition() [2/2]

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

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

With direct access to the global atom array

◆ 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.

◆ 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 modifyPosition or getPosition(AtomNumber)

◆ 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::Analysis::getWeight ( const unsigned &  idata) const
protected

Return the weight of the ith point.

◆ 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::Analysis::isPeriodic ( )
inlinevirtual

Are the base quantities periodic.

Implements PLMD::vesselbase::ActionWithVessel.

◆ lockContributors()

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

◆ lockRequests()

void PLMD::vesselbase::ActionWithAveraging::lockRequests ( )
virtualinherited

Reimplemented from PLMD::ActionAtomistic.

◆ 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.

◆ 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.

◆ modifyGlobalVirial()

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

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

◆ modifyPosition()

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

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

Should be used by action that need to modify the stored atomic coordinates

◆ 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.

◆ noNormalization()

bool PLMD::vesselbase::ActionWithAveraging::noNormalization ( ) const
inlineprotectedinherited

Check if we are using the normalization condition when calculating this quantity.

◆ 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.

◆ parseOutputFile()

void PLMD::analysis::Analysis::parseOutputFile ( const std::string &  key,
std::string &  filename 
)
protected

This is used to read in output file names for analysis methods.

When this method is used and the calculation is not restarted old analysis files are backed up.

◆ 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::Analysis::performAnalysis ( )
pure virtual

◆ performOperations()

void PLMD::analysis::Analysis::performOperations ( const bool &  from_update)
virtual

This does the averaging operation.

Reimplemented from PLMD::vesselbase::ActionWithAveraging.

◆ 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::multicolvar::MultiColvarBase, PLMD::function::FuncPathMSD, PLMD::generic::DumpMassCharge, PLMD::generic::UpdateIf, PLMD::generic::Print, PLMD::generic::Read, PLMD::bias::ReweightTemperature, PLMD::gridtools::ConvertToFES, PLMD::colvar::Energy, and PLMD::colvar::CoordinationBase.

◆ prepareForAveraging()

virtual void PLMD::vesselbase::ActionWithAveraging::prepareForAveraging ( )
inlinevirtualinherited

◆ readAtomsFromPDB() [1/2]

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

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.

◆ readDataFromFile()

void PLMD::analysis::Analysis::readDataFromFile ( const std::string &  filename)
private

Read in data from a file.

◆ 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::Analysis::registerKeywords ( Keywords keys)
static

Finalize the weights without using the log sums.

◆ requestArguments()

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

Setup the dependencies.

◆ requestAtoms()

void PLMD::ActionAtomistic::requestAtoms ( const std::vector< AtomNumber > &  a)
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.

◆ runAnalysis()

void PLMD::analysis::Analysis::runAnalysis ( )

◆ runFinalJobs()

void PLMD::analysis::Analysis::runFinalJobs ( )
virtual

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 from PLMD::Action.

◆ serialCalculation()

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

Is the calculation being done in serial.

◆ setAveragingAction()

void PLMD::vesselbase::ActionWithAveraging::setAveragingAction ( AveragingVessel av_vessel,
const bool &  usetasks 
)
protectedinherited

Set the averaging action.

◆ 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::vesselbase::ActionWithAveraging::unlockRequests ( )
virtualinherited

Reimplemented from PLMD::ActionAtomistic.

◆ update()

void PLMD::vesselbase::ActionWithAveraging::update ( )
virtualinherited

Update.

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

Reimplemented from PLMD::Action.

◆ 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::Analysis::usingMemory ( ) const
inlineprotected

Are we analyzing each data block separately (if we are not this also returns the old normalization )

◆ 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.

Member Data Documentation

◆ argument_names

std::vector<std::string> PLMD::analysis::Analysis::argument_names
protected

List of argument names.

◆ atoms

Atoms& PLMD::ActionAtomistic::atoms
protectedinherited

◆ bridgeVariable

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

This is used for numerical derivatives of bridge variables.

◆ clearstride

unsigned PLMD::vesselbase::ActionWithAveraging::clearstride
protectedinherited

The frequency with which to clear the grid.

◆ comm

Communicator& PLMD::Action::comm
inherited

◆ contributorsAreUnlocked

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

The terms in the series are locked.

◆ current_args

std::vector<double> PLMD::analysis::Analysis::current_args
private

Tempory vector to store values of arguments.

◆ cweight

double PLMD::vesselbase::ActionWithAveraging::cweight
protectedinherited

◆ data

std::vector<ReferenceConfiguration*> PLMD::analysis::Analysis::data
protected

The data we are going to analyze.

◆ 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

◆ freq

unsigned PLMD::analysis::Analysis::freq
private

The frequency with which we are performing analysis.

◆ idata

unsigned PLMD::analysis::Analysis::idata
private

The piece of data we are inserting.

◆ ignore_reweight

bool PLMD::analysis::Analysis::ignore_reweight
private

If we are reusing data are we ignoring the reweighting in that data.

◆ keywords

const Keywords& PLMD::Action::keywords
inherited

◆ log

Log& PLMD::Action::log
inherited

Reference to the log stream.

◆ logweights

std::vector<double> PLMD::analysis::Analysis::logweights
private

The weights of all the data points.

◆ lweight

double PLMD::vesselbase::ActionWithAveraging::lweight
protectedinherited

The current weight and its logarithm.

◆ metricname

std::string PLMD::analysis::Analysis::metricname
private

The type of metric we are using to measure distances.

◆ multi_sim_comm

Communicator& PLMD::Action::multi_sim_comm
inherited

◆ mydata

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

A pointer to the object that stores data.

◆ mydatastash

Analysis* PLMD::analysis::Analysis::mydatastash
private

The Analysis action that we are reusing data from.

◆ ndata

unsigned PLMD::analysis::Analysis::ndata
private

Number of data point we need to run analysis.

◆ needeng

bool PLMD::analysis::Analysis::needeng
private

Do we need the energy (are we reweighting at a different temperature)

◆ nomemory

bool PLMD::analysis::Analysis::nomemory
private

Are we treating each block of data separately.

◆ ofmt

std::string PLMD::analysis::Analysis::ofmt
private

Have we analyzed the data for the first time.

The value of the old normalization constant The format to use in output files

◆ plumed

PlumedMain& PLMD::Action::plumed
inherited

Reference to main plumed object.

◆ reusing_data

bool PLMD::analysis::Analysis::reusing_data
private

Are we reusing data stored by another analysis action.

◆ rfile

OFile PLMD::analysis::Analysis::rfile
private

The checkpoint file.

◆ rtemp

double PLMD::analysis::Analysis::rtemp
private

The temperature at which we want the histogram.

◆ simtemp

double PLMD::analysis::Analysis::simtemp
private

The temperature at which we are running the calculation.

◆ taskFlags

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

This list is used to update the neighbor list.

◆ useRunAllTasks

bool PLMD::vesselbase::ActionWithAveraging::useRunAllTasks
protectedinherited

This ensures runAllTasks is used.

◆ weightHasDerivatives

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

Does the weight have derivatives.

◆ write_chq

bool PLMD::analysis::Analysis::write_chq
private

Are we writing a checkpoint file.


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