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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
 
typedef std::set< FILE * >
::iterator 
files_iterator
 

Public Member Functions

 Analysis (const ActionOptions &)
 
 ~Analysis ()
 
void prepare ()
 Prepare an Action for calculation This can be used by Action if they need some special preparation before calculation. More...
 
void calculate ()
 Calculate an Action. More...
 
void update ()
 Update. More...
 
void accumulate ()
 
virtual void performAnalysis ()=0
 
void apply ()
 Apply an Action. More...
 
void runFinalJobs ()
 RunFinalJobs This method is called once at the very end of the calculation. More...
 
void runAnalysis ()
 
void lockRequests ()
 
void unlockRequests ()
 
void calculateNumericalDerivatives (ActionWithValue *a=NULL)
 N.B. More...
 
bool isPeriodic ()
 Are the base quantities periodic. More...
 
unsigned getNumberOfDerivatives ()
 Get the number of derivatives for final calculated quantity. More...
 
bool onStep () const
 Check if the action is active on this step. 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...
 
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...
 
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...
 
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...
 
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...
 
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...
 
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 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 clearOutputForces ()
 
void calculateAtomicNumericalDerivatives (ActionWithValue *a, const unsigned &startnum)
 Numerical derivative routine to use when using Actions that inherit from BOTH ActionWithArguments and ActionAtomistic. More...
 
void retrieveAtoms ()
 
void applyForces ()
 
const std::set< AtomNumber > & getUnique () const
 
void readAtomsFromPDB (const PDB &pdb)
 Read in an input file containing atom positions and calculate the action for the atomic configuration therin. More...
 
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...
 
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 unlockContributors ()
 
void lockContributors ()
 
virtual void finishTaskListUpdate ()
 
virtual void deactivate_task ()
 Activate the jth colvar Deactivate the current task in future loops. More...
 
void chainRuleForElementDerivatives (const unsigned &, const unsigned &, const double &, Vessel *)
 Merge the derivatives. More...
 
void chainRuleForElementDerivatives (const unsigned &, const unsigned &, const unsigned &, const unsigned &, const double &, Vessel *)
 
virtual void mergeDerivatives (const unsigned &ider, const double &df)
 
virtual void clearDerivativesAfterTask (const unsigned &)
 
bool derivativesAreRequired () const
 Are derivatives required for this quantity. More...
 
virtual void finishComputations ()
 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 ()
 Get the number of quantities that are calculated during each task. More...
 
virtual void getIndexList (const unsigned &ntotal, const unsigned &jstore, const unsigned &maxder, std::vector< unsigned > &indices)
 Get the list of indices that have derivatives. More...
 
void activateTheseTasks (std::vector< bool > &addtionalTasks)
 Switch on additional tasks. 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...
 
virtual void performTask ()=0
 Get the index for a particular numbered task. More...
 
void setElementDerivative (const unsigned &, const double &)
 Set the derivative of the jth element wrt to a numbered element. More...
 
void addElementDerivative (const unsigned &, const double &)
 Add some derivative of the quantity in the sum wrt to a numbered element. More...
 
void setElementValue (const unsigned &, const double &)
 Set the value of the element. More...
 
void addElementValue (const unsigned &, const double &)
 Add to an element value. More...
 
double getElementValue (const unsigned &ival) const
 Get the value of this element. More...
 
double getElementDerivative (const unsigned &) const
 Retrieve the derivative of the quantity in the sum wrt to a numbered element. More...
 
virtual StoreDataVesselbuildDataStashes ()
 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...
 
virtual void activateIndexes (const unsigned &, const unsigned &, const std::vector< unsigned > &)
 These are overwritten in MultiColvarFunction. More...
 
VesselgetVesselWithName (const std::string &mynam)
 Return a particular named vessel. More...
 

Static Public Member Functions

static void registerKeywords (Keywords &keys)
 

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 getNumberOfArguments () const
 Return the number of arguments (this overwrites the one in ActionWithArguments) 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...
 
double getNormalization () const
 Return the normalization constant. More...
 
double getTemp () const
 Return the set temperature (N.B. k_B T is what is returned by this function) More...
 
bool usingMemory () const
 Are we analyzing each data block separately (if we are not this also returns the old normalization ) More...
 
void finalizeWeights (const bool &ignore_weights)
 Convert the stored log weights to proper weights. More...
 
std::vector< Value * > getArguments ()
 Overwrite ActionWithArguments getArguments() so that we don't return the bias. More...
 
std::string getOutputFormat () const
 Return the format to use for numbers in output files. More...
 
int getStride () const
 
void expandArgKeywordInPDB (PDB &pdb)
 This changes the arg keyword in the pdb file. More...
 
void setMaximumNumberOfDerivatives (const unsigned &)
 Set the maximum number of derivatives. 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...
 
unsigned getNumberOfVessels () const
 Get the number of vessels. More...
 
VesselgetPntrToVessel (const unsigned &i)
 Get a pointer to the ith vessel. More...
 
void runAllTasks ()
 Calculate the values of all the vessels. More...
 
void resizeFunctions ()
 Resize all the functions when the number of derivatives change. More...
 
bool calculateAllVessels ()
 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...
 
void accumulateDerivative (const unsigned &ider, const double &df)
 This is used to accumulate the derivatives when we merge using chainRuleForElementDerivatives. More...
 
void clearAfterTask ()
 Clear tempory data that is calculated for each task. 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...
 
unsigned getCurrentNumberOfActiveTasks () const
 Get the number of tasks that are currently active. More...
 
unsigned getActiveTask (const unsigned &ii) const
 Get the ith of the currently active tasks. More...
 
unsigned getPositionInFullTaskList (const unsigned &ii) const
 Get the position of the ith active task in the full list. More...
 
unsigned getCurrentPositionInTaskList () const
 Get the current task's position in the task list. More...
 
unsigned getCurrentTask () const
 Return the number that provides instructions for the current task. More...
 
void deactivateAllTasks ()
 Deactivate all the tasks in the task list. More...
 
void deactivateTasksInRange (const unsigned &lower, const unsigned &upper)
 Deactivate all tasks with i in lower \(\le\) i < upper. More...
 
void addTaskToList (const unsigned &taskCode)
 Add a task to the full list. More...
 

Protected Attributes

std::vector
< ReferenceConfiguration * > 
data
 The data we are going to analyze. More...
 
Atomsatoms
 
std::vector< bool > thisval_wasset
 A boolean that makes sure we don't accumulate very wrong derivatives. 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...
 

Private Member Functions

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

Private Attributes

bool single_run
 Are we running only once for the whole trajectory. More...
 
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...
 
std::vector< Value * > biases
 The biases we are using in reweighting and the args we store them separately. More...
 
unsigned idata
 The piece of data we are inserting. More...
 
std::vector< double > logweights
 The weights of all the data points. More...
 
bool firstAnalysisDone
 Have we analyzed the data for the first time. More...
 
double norm
 The value of the old normalization constant. More...
 
double old_norm
 
std::string ofmt
 The format to use in output files. More...
 
std::vector< double > current_args
 Tempory vector to store values of arguments. More...
 
std::vector< std::string > argument_names
 List of argument names. 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

typedef std::vector<Action*> PLMD::Action::Dependencies
inherited
typedef std::set<FILE*>::iterator PLMD::Action::files_iterator
inherited

Constructor & Destructor Documentation

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

Member Function Documentation

void PLMD::analysis::Analysis::accumulate ( )
void PLMD::vesselbase::ActionWithVessel::accumulateDerivative ( const unsigned &  ider,
const double &  df 
)
inlineprotectedinherited

This is used to accumulate the derivatives when we merge using chainRuleForElementDerivatives.

void PLMD::Action::activate ( )
virtualinherited

Set action to active.

virtual void PLMD::vesselbase::ActionWithVessel::activateIndexes ( const unsigned &  ,
const unsigned &  ,
const std::vector< unsigned > &   
)
inlinevirtualinherited

These are overwritten in MultiColvarFunction.

Reimplemented in PLMD::multicolvar::MultiColvarBase.

void PLMD::vesselbase::ActionWithVessel::activateTheseTasks ( std::vector< bool > &  addtionalTasks)
inherited

Switch on additional tasks.

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

Add a bridging vessel to the list of vessels.

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

Specify that this Action depends on another one.

void PLMD::vesselbase::ActionWithVessel::addElementDerivative ( const unsigned &  ider,
const double &  der 
)
inlineinherited

Add some derivative of the quantity in the sum wrt to a numbered element.

void PLMD::vesselbase::ActionWithVessel::addElementValue ( const unsigned &  ival,
const double &  val 
)
inlineinherited

Add to an element value.

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

Add forces to arguments (used in apply)

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

Add a task to the full list.

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.

void PLMD::vesselbase::ActionWithVessel::addVessel ( Vessel vv)
protectedinherited
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.

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::ActionVolume, and PLMD::manyrestraints::ManyRestraintsBase.

void ActionAtomistic::applyForces ( )
inherited
double PLMD::ActionWithArguments::bringBackInPbc ( int  i,
double  d1 
) const
inlineinherited

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

StoreDataVessel * PLMD::vesselbase::ActionWithVessel::buildDataStashes ( )
virtualinherited

Ensure that data required in other vessels is stored.

Reimplemented in PLMD::multicolvar::MultiColvarBase, and PLMD::crystallization::VectorMultiColvar.

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

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.

bool PLMD::vesselbase::ActionWithVessel::calculateAllVessels ( )
protectedinherited

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

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

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

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

void PLMD::analysis::Analysis::calculateNumericalDerivatives ( ActionWithValue a = NULL)
inlinevirtual

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.

void PLMD::vesselbase::ActionWithVessel::chainRuleForElementDerivatives ( const unsigned &  iout,
const unsigned &  ider,
const double &  df,
Vessel valout 
)
inherited

Merge the derivatives.

void PLMD::vesselbase::ActionWithVessel::chainRuleForElementDerivatives ( const unsigned &  iout,
const unsigned &  ider,
const unsigned &  stride,
const unsigned &  off,
const double &  df,
Vessel valout 
)
inherited
void ActionAtomistic::changeBox ( const Tensor newbox)
inherited

Change the box shape.

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

Check if the action needs gradient.

Reimplemented in PLMD::bias::MetaD, and PLMD::generic::DumpProjections.

virtual bool PLMD::Action::checkNumericalDerivatives ( ) const
inlinevirtualinherited

Check if numerical derivatives should be performed.

Reimplemented in PLMD::ActionWithValue.

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

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

Cite a paper see PlumedMain::cite.

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

Clear tempory data that is calculated for each task.

void PLMD::Action::clearDependencies ( )
inherited

Clear the dependence list for this Action.

void PLMD::vesselbase::ActionWithVessel::clearDerivativesAfterTask ( const unsigned &  ider)
virtualinherited
void PLMD::Action::clearOptions ( )
virtualinherited
void ActionAtomistic::clearOutputForces ( )
inherited
void PLMD::Action::deactivate ( )
inlinevirtualinherited

Set action to inactive.

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

Activate the jth colvar Deactivate the current task in future loops.

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

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

Deactivate all the tasks in the task list.

void PLMD::vesselbase::ActionWithVessel::deactivateTasksInRange ( const unsigned &  lower,
const unsigned &  upper 
)
protectedinherited

Deactivate all tasks with i in lower \(\le\) i < upper.

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

Are derivatives required for this quantity.

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

Takes the difference taking into account pbc for arg i.

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

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.

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

Crash calculation and print documentation.

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

Exit with error code c.

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

This changes the arg keyword in the pdb file.

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

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

void PLMD::Action::fflush ( )
inherited

Tell to the Action to flush open files.

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

Convert the stored log weights to proper weights.

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

Finish running all the calculations.

virtual void PLMD::vesselbase::ActionWithVessel::finishTaskListUpdate ( )
inlinevirtualinherited
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)
AtomNumber PLMD::ActionAtomistic::getAbsoluteIndex ( int  i) const
inlineinherited

Get the absolute index of an atom.

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

Get the vector of absolute indexes.

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

Get the ith of the currently active tasks.

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

Returns the value of an argument.

std::vector< Value * > PLMD::analysis::Analysis::getArguments ( )
inlineprotected

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

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

Get box shape.

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

Get charge of i-th atom.

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

Get the number of tasks that are currently active.

unsigned PLMD::vesselbase::ActionWithVessel::getCurrentPositionInTaskList ( ) const
inlineprotectedinherited

Get the current task's position in the task list.

unsigned PLMD::vesselbase::ActionWithVessel::getCurrentTask ( ) const
inlineprotectedinherited

Return the number that provides instructions for the current task.

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

Retrieve the ith point.

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

Return dependencies.

std::string PLMD::Action::getDocumentation ( ) const
virtualinherited
double PLMD::vesselbase::ActionWithVessel::getElementDerivative ( const unsigned &  ider) const
inlineinherited

Retrieve the derivative of the quantity in the sum wrt to a numbered element.

double PLMD::vesselbase::ActionWithVessel::getElementValue ( const unsigned &  ival) const
inlineinherited

Get the value of this element.

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

Get energy.

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

Check if we are on an exchange step.

bool PLMD::vesselbase::ActionWithVessel::getForcesFromVessels ( std::vector< double > &  forcesToApply)
protectedinherited

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

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

Get the full size of the taskList dynamic list.

void PLMD::vesselbase::ActionWithVessel::getIndexList ( const unsigned &  ntotal,
const unsigned &  jstore,
const unsigned &  maxder,
std::vector< unsigned > &  indices 
)
virtualinherited

Get the list of indices that have derivatives.

Reimplemented in PLMD::multicolvar::MultiColvarBase, and PLMD::multicolvar::Density.

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

Returns the label.

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

Get mass of i-th atom.

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

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

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

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

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

Returns the name.

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

Return the value for the neighbor list tolerance.

double PLMD::analysis::Analysis::getNormalization ( ) const
protected

Return the normalization constant.

unsigned PLMD::analysis::Analysis::getNumberOfArguments ( ) const
inlineprotected

Return the number of arguments (this overwrites the one in ActionWithArguments)

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

Get number of available atoms.

unsigned PLMD::analysis::Analysis::getNumberOfDataPoints ( ) const
inlineprotected

Return the number of data points.

unsigned PLMD::analysis::Analysis::getNumberOfDerivatives ( )
inlinevirtual

Get the number of derivatives for final calculated quantity.

Implements PLMD::vesselbase::ActionWithVessel.

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

Get the number of vessels.

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

Return the format to use for numbers in output files.

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

Get reference to Pbc.

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.

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

Return a pointer to specific argument.

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

Get a pointer to the ith vessel.

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

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

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

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

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

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

Get the array of all positions.

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

Get the scalar product between the gradients of two variables.

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

Return the present timestep.

int PLMD::ActionPilot::getStride ( ) const
protectedinherited
double PLMD::analysis::Analysis::getTemp ( ) const
protected

Return the set temperature (N.B. k_B T is what is returned by this function)

double PLMD::Action::getTime ( ) const
inherited

Return the present time.

double PLMD::Action::getTimeStep ( ) const
inherited

Return the timestep.

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

Return the value of the tolerance.

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)

const std::set< AtomNumber > & PLMD::ActionAtomistic::getUnique ( ) const
inlineinherited
Vessel * PLMD::vesselbase::ActionWithVessel::getVesselWithName ( const std::string &  mynam)
inherited

Return a particular named vessel.

double PLMD::analysis::Analysis::getWeight ( const unsigned &  idata) const
protected

Return the weight of the ith point.

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.

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

Check if action is active.

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

Check if an option is on.

bool PLMD::analysis::Analysis::isPeriodic ( )
inlinevirtual

Are the base quantities periodic.

Implements PLMD::vesselbase::ActionWithVessel.

void PLMD::vesselbase::ActionWithVessel::lockContributors ( )
inherited
void PLMD::analysis::Analysis::lockRequests ( )
inlinevirtual

Reimplemented from PLMD::Action.

void PLMD::vesselbase::ActionWithVessel::mergeDerivatives ( const unsigned &  ider,
const double &  df 
)
virtualinherited
double & PLMD::ActionAtomistic::modifyForceOnEnergy ( )
inlineinherited

Get a reference to force on energy.

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

Get a reference to forces array.

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

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

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

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

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

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

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

Get a reference to virial array.

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

Turn on the derivatives in the vessel.

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

Check if the action is active on this step.

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

Parse one keyword as generic type.

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

Parse a list of arguments.

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

Parse a list of atoms without a numbered keyword.

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

Parse an list of atom with a numbred keyword.

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

Parse one keyword as boolean flag.

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

Parse one numbered keyword as generic type.

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.

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.

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

Parse one keyword as std::vector.

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

Compute the pbc distance between two positions.

virtual void PLMD::analysis::Analysis::performAnalysis ( )
pure virtual
virtual void PLMD::vesselbase::ActionWithVessel::performTask ( )
pure virtualinherited
void PLMD::analysis::Analysis::prepare ( )
virtual

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 from PLMD::Action.

void 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.

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.

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

Read in data from a file.

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

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

void PLMD::analysis::Analysis::registerKeywords ( Keywords keys)
static
void PLMD::ActionWithArguments::requestArguments ( const std::vector< Value * > &  arg)
inherited

Setup the dependencies.

void 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

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

Resize all the functions when the number of derivatives change.

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

What are the domains of the base quantities.

Reimplemented in PLMD::multicolvar::Torsions.

double PLMD::analysis::Analysis::retrieveNorm ( ) const
inlineprivate

This retrieves the value of norm from the analysis action.

It is only used to transfer data from one analysis action to another. You should never need to use it. If you think you need it you probably need getNormalization()

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

Calculate the values of all the vessels.

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

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

Is the calculation being done in serial.

void PLMD::vesselbase::ActionWithVessel::setElementDerivative ( const unsigned &  ider,
const double &  der 
)
inlineinherited

Set the derivative of the jth element wrt to a numbered element.

void PLMD::vesselbase::ActionWithVessel::setElementValue ( const unsigned &  ival,
const double &  val 
)
inlineinherited

Set the value of the element.

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

Add the forces to the atoms.

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

Set that we are using low memory.

void PLMD::vesselbase::ActionWithVessel::setMaximumNumberOfDerivatives ( const unsigned &  )
protectedinherited

Set the maximum number of derivatives.

void PLMD::Action::setOption ( const std::string &  s)
virtualinherited
void PLMD::vesselbase::ActionWithVessel::unlockContributors ( )
inherited
void PLMD::analysis::Analysis::unlockRequests ( )
inlinevirtual

Reimplemented from PLMD::Action.

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

Update.

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

Reimplemented from PLMD::Action.

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

Are we using low memory.

bool PLMD::analysis::Analysis::usingMemory ( ) const
inlineprotected

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

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

Issue a warning.

Member Data Documentation

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

List of argument names.

Atoms& PLMD::ActionAtomistic::atoms
protectedinherited
std::vector<Value*> PLMD::analysis::Analysis::biases
private

The biases we are using in reweighting and the args we store them separately.

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

This is used for numerical derivatives of bridge variables.

Communicator& PLMD::Action::comm
inherited
bool PLMD::vesselbase::ActionWithVessel::contributorsAreUnlocked
protectedinherited

The terms in the series are locked.

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

Tempory vector to store values of arguments.

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

The data we are going to analyze.

std::set<FILE*> PLMD::Action::files
inherited
bool PLMD::analysis::Analysis::firstAnalysisDone
private

Have we analyzed the data for the first time.

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

The frequency with which we are performing analysis.

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

The piece of data we are inserting.

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

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

const Keywords& PLMD::Action::keywords
inherited
Log& PLMD::Action::log
inherited

Reference to the log stream.

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

The weights of all the data points.

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

The type of metric we are using to measure distances.

Communicator& PLMD::Action::multi_sim_comm
inherited
Analysis* PLMD::analysis::Analysis::mydatastash
private

The Analysis action that we are reusing data from.

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

Number of data point we need to run analysis.

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

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

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

Are we treating each block of data separately.

double PLMD::analysis::Analysis::norm
private

The value of the old normalization constant.

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

The format to use in output files.

double PLMD::analysis::Analysis::old_norm
private
PlumedMain& PLMD::Action::plumed
inherited

Reference to main plumed object.

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

Are we reusing data stored by another analysis action.

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

The checkpoint file.

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

The temperature at which we want the histogram.

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

The temperature at which we are running the calculation.

bool PLMD::analysis::Analysis::single_run
private

Are we running only once for the whole trajectory.

std::vector<bool> PLMD::vesselbase::ActionWithVessel::thisval_wasset
protectedinherited

A boolean that makes sure we don't accumulate very wrong derivatives.

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

Does the weight have derivatives.

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

Are we writing a checkpoint file.


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