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

#include <MetainferenceBase.h>

Inheritance diagram for PLMD::isdb::MetainferenceBase:
Inheritance graph
[legend]

Public Types

typedef std::vector< Action * > Dependencies
 

Public Member Functions

 MetainferenceBase (const ActionOptions &)
 
 ~MetainferenceBase ()
 
virtual void activate ()
 Set action to active. More...
 
void addComponent (const std::string &name)
 Add a value with a name like label.name. More...
 
void addComponentWithDerivatives (const std::string &name)
 Add a value with a name like label.name that has derivatives. More...
 
void addDependency (Action *)
 Specify that this Action depends on another one. More...
 
void addForcesOnArguments (const std::vector< double > &forces)
 Add forces to arguments (used in apply) More...
 
void addValue ()
 Add a value with the name label. More...
 
void addValueWithDerivatives ()
 Add a value with the name label that has derivatives. More...
 
void allowToAccessGlobalForces ()
 Allow calls to modifyGlobalForce() More...
 
void apply () override
 Apply an Action. More...
 
void applyForces ()
 
virtual void beforeUpdate ()
 Before Update. More...
 
double bringBackInPbc (int i, double d1) const
 Takes one value and brings it back into the pbc of argument i. More...
 
virtual void calculate ()=0
 Calculate an Action. More...
 
void calculateAtomicNumericalDerivatives (ActionWithValue *a, const unsigned &startnum)
 Numerical derivative routine to use when using Actions that inherit from BOTH ActionWithArguments and ActionAtomistic. More...
 
void calculateFromPDB (const PDB &)
 Calculate the action given a pdb file as input. More...
 
void calculateNumericalDerivatives (ActionWithValue *a) override
 N.B. More...
 
void changeBox (const Tensor &newbox)
 Change the box shape. More...
 
virtual void checkFieldsAllowed ()
 
virtual bool checkNeedsGradients () const
 Check if the action needs gradient. More...
 
virtual bool checkNumericalDerivatives () const
 Check if numerical derivatives should be performed. More...
 
bool checkNumericalDerivatives () const override
 Check if numerical derivatives should be used. More...
 
void checkRead ()
 Check if Action was properly read. More...
 
bool checkUpdate () const
 Check if action should be updated. More...
 
std::string cite (const std::string &s)
 Cite a paper see PlumedMain::cite. More...
 
void clearDependencies ()
 Clear the dependence list for this Action. More...
 
virtual void clearDerivatives ()
 Clear the derivatives of values wrt parameters. More...
 
void clearInputForces ()
 Clear the forces on the values. More...
 
virtual void clearOptions ()
 
void clearOutputForces ()
 
void componentIsNotPeriodic (const std::string &name)
 Set your value component to have no periodicity. More...
 
void componentIsPeriodic (const std::string &name, const std::string &min, const std::string &max)
 Set the value to be periodic with a particular domain. More...
 
ValuecopyOutput (const std::string &name) const
 Return a pointer to the value with name (this is used to retrieve values in other PLMD::Actions) You should NEVER use this routine to refer to the components of your PLMD::Action. More...
 
ValuecopyOutput (const unsigned &n) const
 Return a pointer to the value with this number (this is used to retrieve values in other PLMD::Actions) You should NEVER use this routine to refer to the components of your PLMD::Action. More...
 
virtual void deactivate ()
 Set action to inactive. More...
 
double difference (int, double, double) const
 Takes the difference taking into account pbc for arg i. More...
 
virtual bool doNotCalculateDerivatives () const
 Are we not calculating derivatives. More...
 
void doNotForce ()
 Skip atom forces - use with care. More...
 
void doNotRetrieve ()
 Skip atom retrieval - use with care. More...
 
void error (const std::string &msg) const
 Crash calculation and print documentation. More...
 
bool exists (const std::string &name) const
 Check if a value with a particular name is present. More...
 
void exit (int c=0)
 Exit with error code c. More...
 
int fclose (FILE *fp)
 Closes a file opened with Action::fclose(). More...
 
void fflush ()
 Tell to the Action to flush open files. More...
 
FILE * fopen (const char *path, const char *mode)
 Opens a file. More...
 
AtomNumber getAbsoluteIndex (int i) const
 Get the absolute index of an atom. More...
 
virtual const std::vector< AtomNumber > & getAbsoluteIndexes () const
 Get the vector of absolute indexes. More...
 
double getArgument (const unsigned n) const
 Returns the value of an argument. More...
 
virtual const std::vector< Value * > & getArguments () const
 Returns an array of pointers to the arguments. More...
 
const TensorgetBox () const
 Get box shape. More...
 
double getCharge (int i) const
 Get charge of i-th atom. More...
 
std::string getComponentsList () const
 get a string that contains all the available components More...
 
std::vector< std::string > getComponentsVector () const
 get a vector that contains the label for all the components More...
 
bool getCPT () const
 Return true if we are doing at a checkpoint step. More...
 
const DependenciesgetDependencies () const
 Return dependencies. More...
 
virtual std::string getDocumentation () const
 
bool getDoScore ()
 
const double & getEnergy () const
 Get energy. More...
 
bool getExchangeStep () const
 Check if we are on an exchange step. More...
 
const VectorgetGlobalPosition (AtomNumber) const
 Get position of i-th atom (access by absolute AtomNumber). More...
 
std::string getKeyword (const std::string &key)
 Just read one of the keywords and return the whole thing as a string. More...
 
const std::string & getLabel () const
 Returns the label. More...
 
double getMass (int i) const
 Get mass of i-th atom. More...
 
double getMetaDer (const unsigned index)
 
const std::string & getName () const
 Returns the name. More...
 
unsigned getNarg ()
 
virtual unsigned getNumberOfArguments () const
 Returns the number of arguments. More...
 
unsigned getNumberOfAtoms () const
 Get number of available atoms. More...
 
int getNumberOfComponents () const
 Returns the number of values defined. More...
 
unsigned getNumberOfDerivatives () override
 
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...
 
double getOutputQuantity (const unsigned j) const
 Get the value of one of the components of the PLMD::Action. More...
 
const PbcgetPbc () const
 Get reference to Pbc. More...
 
ValuegetPntrToArgument (const unsigned n)
 Return a pointer to specific argument. More...
 
const VectorgetPosition (int) const
 Get position of i-th atom (access by relative index) More...
 
const std::vector< Vector > & getPositions () const
 Get the array of all positions. More...
 
double getProjection (unsigned i, unsigned j) const
 Get the scalar product between the gradients of two variables. More...
 
bool getRestart () const
 Return true if we are doing a restart. More...
 
double getScore ()
 
long int getStep () const
 Return the present timestep. More...
 
double getTime () const
 Return the present time. More...
 
double getTimeStep () const
 Return the timestep. More...
 
unsigned getTotAtoms () const
 Get total number of atoms, including virtual ones. More...
 
const std::set< AtomNumber > & getUnique () const
 
const std::set< AtomNumber > & getUniqueLocal () const
 
unsigned getWstride ()
 
void Initialise (const unsigned input)
 
void interpretArgumentList (const std::vector< std::string > &c, std::vector< Value * > &arg)
 Convert a list of argument names into a list of pointers to the values. More...
 
void interpretAtomList (std::vector< std::string > &strings, std::vector< AtomNumber > &t)
 Convert a set of read in strings into an atom list (this is used in parseAtomList) More...
 
bool isActive () const
 Check if action is active. More...
 
bool isOptionOn (const std::string &s) const
 Check if an option is on. More...
 
void lockRequests () override
 
void makeWhole ()
 Make atoms whole, assuming they are in the proper order. More...
 
double & modifyForceOnEnergy ()
 Get a reference to force on energy. More...
 
double & modifyForceOnExtraCV ()
 Get a reference to force on extraCV. More...
 
std::vector< Vector > & modifyForces ()
 Get a reference to forces array. More...
 
VectormodifyGlobalForce (AtomNumber)
 Get modifiable force of i-th atom (access by absolute AtomNumber). More...
 
PbcmodifyGlobalPbc ()
 Get modifiable PBC Should be used by action that need to modify the stored box. More...
 
VectormodifyGlobalPosition (AtomNumber)
 Get modifiable position of i-th atom (access by absolute AtomNumber). More...
 
TensormodifyGlobalVirial ()
 Get modifiable virial Should be used by action that need to modify the stored virial. More...
 
TensormodifyVirial ()
 Get a reference to virial array. More...
 
template<class T >
void parse (const std::string &key, T &t)
 Parse one keyword as generic type. More...
 
bool parseArgumentList (const std::string &key, int i, std::vector< Value * > &args)
 Parse a numbered list of arguments. More...
 
void parseArgumentList (const std::string &key, std::vector< Value * > &args)
 Parse a list of arguments. 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 parseAtomList (const std::string &key, std::vector< AtomNumber > &t)
 Parse a list of atoms without a numbered keyword. More...
 
void parseFlag (const std::string &key, bool &t)
 Parse one keyword as boolean flag. More...
 
template<class T >
bool parseNumbered (const std::string &key, const int no, T &t)
 Parse one numbered keyword as generic type. More...
 
template<class T >
bool parseNumberedVector (const std::string &key, const int no, std::vector< T > &t)
 Parse a vector with a number. More...
 
template<class T >
void parseVector (const std::string &key, std::vector< T > &t)
 Parse one keyword as std::vector. More...
 
void pbcApply (std::vector< Vector > &dlist, unsigned max_index=0) const
 Applies PBCs to a seriens of positions or distances. More...
 
Vector pbcDistance (const Vector &, const Vector &) const
 Compute the pbc distance between two positions. More...
 
virtual void prepare ()
 Prepare an Action for calculation This can be used by Action if they need some special preparation before calculation. More...
 
void readAtomsFromPDB (const PDB &pdb) override
 Read in an input file containing atom positions and calculate the action for the atomic configuration therin. More...
 
void requestArguments (const std::vector< Value * > &arg)
 Setup the dependencies. More...
 
void requestAtoms (const std::vector< AtomNumber > &a, const bool clearDep=true)
 Request an array of atoms. More...
 
void requestExtraDependencies (const std::vector< Value * > &extra)
 
virtual void retrieveAtoms ()
 
virtual void runFinalJobs ()
 RunFinalJobs This method is called once at the very end of the calculation. More...
 
void Selector ()
 
void setArgDerivatives (Value *v, const double &d)
 
void setAtomsDerivatives (Value *v, const unsigned i, const Vector &d)
 
void setBoxDerivatives (Value *v, const Tensor &d)
 
void setCalcData (const std::vector< double > &data)
 
void setCalcData (const unsigned index, const double datum)
 
void setDerivatives ()
 
void setForcesOnAtoms (const std::vector< double > &forcesToApply, unsigned ind=0)
 Add the forces to the atoms. More...
 
void setGradientsIfNeeded ()
 Calculate the gradients and store them for all the values (need for projections) More...
 
void setNarg (const unsigned input)
 
void setNotPeriodic ()
 Set your default value to have no periodicity. More...
 
virtual void setOption (const std::string &s)
 
void setParameter (const double input)
 
void setParameters (const std::vector< double > &input)
 
void setPeriodic (const std::string &min, const std::string &max)
 Set the value to be periodic with a particular domain. More...
 
void setScore (const double score)
 
void setValue (Value *, double)
 Set the value. More...
 
void turnOnDerivatives () override
 Activate the calculation of derivatives. More...
 
void unlockRequests () override
 
virtual void update ()
 Update. More...
 
void updateUniqueLocal ()
 updates local unique atoms More...
 
void useNumericalDerivatives ()
 This forces the class to use numerical derivatives. More...
 
void warning (const std::string &msg)
 Issue a warning. More...
 
void writeStatus ()
 

Static Public Member Functions

static void componentsAreNotOptional (Keywords &keys)
 Puts a message into the manual that the components always output. More...
 
static void noAnalyticalDerivatives (Keywords &keys)
 Insist that numerical derivatives should always be used for an action and make this fact appear in the manual. More...
 
static void registerKeywords (Keywords &keys)
 
static void useCustomisableComponents (Keywords &keys)
 The components in the action will depend on the user. More...
 

Public Attributes

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

Protected Member Functions

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

Protected Attributes

Atomsatoms
 

Private Types

enum  {
  GAUSS, MGAUSS, OUTLIERS, MOUTLIERS,
  GENERIC
}
 
enum  { LIKE_GAUSS, LIKE_LOGN }
 
enum  { SC_GAUSS, SC_FLAT }
 

Private Member Functions

void do_regression_zero (const std::vector< double > &mean)
 
double doMonteCarlo (const std::vector< double > &mean)
 
void get_sigma_mean (const double weight, const double norm, const double neff, const std::vector< double > &mean)
 
void get_weights (double &weight, double &norm, double &neff)
 
double getCalcData (const unsigned index)
 
int getComponent (const std::string &name) const
 Return the index for the component named name. More...
 
void getEnergyForceGJ (const std::vector< double > &mean, const std::vector< double > &dmean_x, const std::vector< double > &dmean_b)
 
void getEnergyForceGJE (const std::vector< double > &mean, const std::vector< double > &dmean_x, const std::vector< double > &dmean_b)
 
void getEnergyForceMIGEN (const std::vector< double > &mean, const std::vector< double > &dmean_x, const std::vector< double > &dmean_b)
 
void getEnergyForceSP (const std::vector< double > &mean, const std::vector< double > &dmean_x, const std::vector< double > &dmean_b)
 
void getEnergyForceSPE (const std::vector< double > &mean, const std::vector< double > &dmean_x, const std::vector< double > &dmean_b)
 
double getEnergyGJ (const std::vector< double > &mean, const std::vector< double > &sigma, const double scale, const double offset)
 
double getEnergyGJE (const std::vector< double > &mean, const std::vector< double > &sigma, const double scale, const double offset)
 
double getEnergyMIGEN (const std::vector< double > &mean, const std::vector< double > &ftilde, const std::vector< double > &sigma, const double scale, const double offset)
 
double getEnergySP (const std::vector< double > &mean, const std::vector< double > &sigma, const double scale, const double offset)
 
double getEnergySPE (const std::vector< double > &mean, const std::vector< double > &sigma, const double scale, const double offset)
 
void moveScaleOffset (const std::vector< double > &mean_, double &old_energy)
 
void moveSigmas (const std::vector< double > &mean_, double &old_energy, const unsigned i, const std::vector< unsigned > &indices, bool &breaknow)
 
void moveTilde (const std::vector< double > &mean_, double &old_energy)
 
void replica_averaging (const double weight, const double norm, std::vector< double > &mean, std::vector< double > &dmean_b)
 
void setMetaDer (const unsigned index, const double der)
 

Private Attributes

bool active
 Switch to activate Action on this step. More...
 
Dependencies after
 Actions on which this Action depends. More...
 
std::vector< Value * > arguments
 
std::vector< std::vector< double > > average_weights_
 
std::vector< double > calc_data_
 
std::vector< double > charges
 
bool chargesWereSet
 
double decay_w_
 
double Dftilde_
 
unsigned do_optsigmamean_
 
bool do_reweight_
 
bool doCheckPoint
 
double Doffset_
 
bool donotforce
 
bool donotretrieve
 
bool dooffset_
 
bool doregres_zero_
 
bool doscale_
 
bool doscore_
 
double Dscale_
 
std::vector< double > Dsigma_
 
double energy
 
std::string extraCV
 
bool firstTime
 
std::vector< bool > firstTimeW
 
double forceOnEnergy
 
double forceOnExtraCV
 
std::vector< double > forces
 
std::vector< double > forcesToApply
 
std::vector< double > ftilde_
 
unsigned gen_likelihood_
 
std::vector< AtomNumberindexes
 
unsigned iselect
 
double kbt_
 
std::string label
 Label of the Action, as set with LABEL= in the plumed.dat file. More...
 
std::vector< std::string > line
 Directive line. More...
 
bool lockRequestArguments
 
bool lockRequestAtoms
 
std::vector< double > masses
 
bool master
 
long unsigned MCaccept_
 
long unsigned MCacceptFT_
 
long unsigned MCacceptScale_
 
unsigned MCchunksize_
 
unsigned MCsteps_
 
long unsigned MCtrial_
 
std::vector< double > metader_
 
unsigned N_optimized_step_
 
const std::string name
 Name of the directive in the plumed.dat file. More...
 
unsigned narg
 
bool noderiv
 Are we skipping the calculation of the derivatives. More...
 
unsigned noise_type_
 
int nregres_zero_
 
unsigned nrep_
 
unsigned nsel_
 
bool numericalDerivatives
 Are we using numerical derivatives to differentiate. More...
 
double offset_
 
double offset_max_
 
double offset_min_
 
double offset_mu_
 
unsigned offset_prior_
 
unsigned optimized_step_
 
std::set< std::string > options
 Option that you might have enabled. More...
 
unsigned optsigmamean_stride_
 
std::vector< double > parameters
 
Pbcpbc =*pbc_fwd
 
ForwardDecl< Pbcpbc_fwd
 
std::vector< Vectorpositions
 
std::vector< Randomrandom
 
unsigned replica_
 
int replica_index
 
bool restart
 
double scale_
 
double scale_max_
 
double scale_min_
 
double scale_mu_
 
unsigned scale_prior_
 
std::string selector_
 
OFile sfile_
 
std::vector< double > sigma_
 
std::vector< double > sigma_max_
 
std::vector< double > sigma_max_est_
 
std::vector< double > sigma_mean2_
 
std::vector< std::vector< std::vector< double > > > sigma_mean2_last_
 
std::vector< double > sigma_min_
 
bool sigmamax_opt_done_
 
std::string status_file_name_
 
std::set< AtomNumberunique
 unique should be an ordered set since we later create a vector containing the corresponding indexes More...
 
std::set< AtomNumberunique_local
 unique_local should be an ordered set since we later create a vector containing the corresponding indexes More...
 
double update_from
 Update only after this time. More...
 
double update_until
 Update only until this time. More...
 
ValuevalueAccept
 
ValuevalueAcceptFT
 
ValuevalueAcceptScale
 
std::vector< Value * > valueFtilde
 
ValuevalueOffset
 
std::vector< std::unique_ptr< Value > > values
 An array containing the values for this action. More...
 
ValuevalueScale
 
ValuevalueScore
 
std::vector< Value * > valueSigma
 
std::vector< Value * > valueSigmaMean
 
Tensor virial
 
unsigned write_stride_
 

Detailed Description

This is the abstract base class to use for implementing new ISDB Metainference actions, within it there is information as to how to go about implementing a new Metainference action.

Member Typedef Documentation

◆ Dependencies

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

Member Enumeration Documentation

◆ anonymous enum

anonymous enum
private
Enumerator
GAUSS 
MGAUSS 
OUTLIERS 
MOUTLIERS 
GENERIC 

◆ anonymous enum

anonymous enum
private
Enumerator
LIKE_GAUSS 
LIKE_LOGN 

◆ anonymous enum

anonymous enum
private
Enumerator
SC_GAUSS 
SC_FLAT 

Constructor & Destructor Documentation

◆ MetainferenceBase()

PLMD::isdb::MetainferenceBase::MetainferenceBase ( const ActionOptions ao)
explicit

◆ ~MetainferenceBase()

PLMD::isdb::MetainferenceBase::~MetainferenceBase ( )

Member Function Documentation

◆ activate()

void PLMD::Action::activate ( )
virtualinherited

Set action to active.

◆ 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)

◆ 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.

◆ allowToAccessGlobalForces()

void PLMD::ActionAtomistic::allowToAccessGlobalForces ( )
inlineinherited

Allow calls to modifyGlobalForce()

◆ apply()

void PLMD::isdb::MetainferenceBase::apply ( )
inlineoverridevirtual

Apply an Action.

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

Implements PLMD::Action.

◆ 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.

◆ calculate()

virtual void PLMD::Action::calculate ( )
pure virtualinherited

Calculate an Action.

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

Implemented in PLMD::bias::MetaD, PLMD::isdb::CS2Backbone, PLMD::bias::PBMetaD, PLMD::ves::VesLinearExpansion, PLMD::isdb::EMMI, PLMD::isdb::Metainference, PLMD::opes::OPESmetad< mode >, PLMD::isdb::RDC, PLMD::function::FuncPathMSD, PLMD::generic::FitToTemplate, PLMD::function::FuncSumHills, PLMD::mapping::PCAVars, PLMD::ves::Optimizer, PLMD::ves::BasisFunctions, PLMD::ves::TargetDistribution, PLMD::function::Custom, PLMD::ves::VesDeltaF, PLMD::opes::OPESexpanded, PLMD::multicolvar::MultiColvarBase, PLMD::generic::Plumed, PLMD::generic::WrapAround, PLMD::generic::Include, PLMD::bias::MaxEnt, PLMD::generic::Group, PLMD::generic::DumpAtoms, PLMD::isdb::SAXS, PLMD::vatom::Center, PLMD::colvar::Dimer, PLMD::bias::ExtendedLagrangian, PLMD::colvar::DRMSD, PLMD::bias::External, PLMD::generic::EffectiveEnergyDrift, PLMD::colvar::Distance, PLMD::colvar::ContactMap, PLMD::generic::WholeMolecules, PLMD::bias::MovingRestraint, PLMD::colvar::ERMSD, PLMD::mapping::AdaptivePath, PLMD::ves::OutputFesBias, PLMD::function::Target, PLMD::adjmat::Sprint, PLMD::generic::ResetCell, PLMD::isdb::JCoupling, PLMD::generic::Read, PLMD::colvar::EEFSolv, PLMD::analysis::Average, PLMD::analysis::AnalysisBase, PLMD::colvar::Torsion, PLMD::multicolvar::CenterOfMultiColvar, PLMD::vatom::FixedAtom, PLMD::colvar::PathMSDBase, PLMD::bias::ABMD, PLMD::generic::DumpMassCharge, PLMD::multicolvar::DistanceFromContour, PLMD::isdb::FretEfficiency, PLMD::ves::OutputBasisFunctions, PLMD::colvar::Gyration, PLMD::generic::UpdateIf, PLMD::colvar::Angle, PLMD::generic::Print, PLMD::ves::OutputTargetDistribution, PLMD::function::Combine, PLMD::isdb::PRE, PLMD::adjmat::OutputCluster, PLMD::function::LocalEnsemble, PLMD::colvar::Position, PLMD::secondarystructure::SecondaryStructureRMSD, PLMD::generic::RandomExchanges, PLMD::adjmat::ClusterDistribution, PLMD::bias::BiasValue, PLMD::isdb::NOE, PLMD::multicolvar::DumpMultiColvar, PLMD::maze::Loss, PLMD::colvar::Puckering, PLMD::function::Piecewise, PLMD::adjmat::ClusterDiameter, PLMD::analysis::Committor, PLMD::adjmat::ClusterSize, PLMD::bias::LWalls, PLMD::bias::UWalls, PLMD::adjmat::ClusterProperties, PLMD::colvar::Energy, PLMD::generic::Flush, PLMD::isdb::Selector, PLMD::colvar::Dipole, PLMD::multicolvar::BridgedMultiColvarFunction, PLMD::bias::Restraint, PLMD::function::Ensemble, PLMD::colvar::Constant, PLMD::function::Stats, PLMD::generic::DumpDerivatives, PLMD::GenericMolInfo, PLMD::generic::DumpForces, PLMD::generic::EndPlumed, PLMD::manyrestraints::ManyRestraintsBase, PLMD::colvar::ExtraCV, PLMD::function::Sort, PLMD::generic::Debug, PLMD::generic::DumpProjections, PLMD::vatom::Ghost, PLMD::adjmat::DumpGraph, PLMD::colvar::Template, PLMD::colvar::Cell, PLMD::opes::ExpansionCVs, PLMD::gridtools::ActionWithGrid, PLMD::adjmat::ClusteringBase, PLMD::colvar::Volume, PLMD::generic::Time, PLMD::colvar::ColvarFake, PLMD::ActionShortcut, PLMD::colvar::CoordinationBase, PLMD::bias::ReweightBase, PLMD::colvar::MultiRMSD, PLMD::colvar::PCARMSD, PLMD::colvar::RMSD, PLMD::ActionAnyorder, PLMD::ActionSetup, PLMD::gridtools::GridPrintingBase, PLMD::mapping::PathBase, PLMD::logmfd::LogMFD, PLMD::eds::EDS, PLMD::piv::PIV, PLMD::fisst::FISST, PLMD::sasa::SASA_HASEL, PLMD::sasa::SASA_LCPO, PLMD::isdb::Rescale, PLMD::maze::OptimizerBias, PLMD::funnel::Funnel, PLMD::function::FuncPathGeneral, PLMD::funnel::FUNNEL_PS, PLMD::function::annfunc::ANN, PLMD::isdb::Caliber, PLMD::maze::Optimizer, PLMD::colvar::ProjectionOnAxis, PLMD::s2cm::S2ContactModel, and PLMD::isdb::Select.

◆ 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::isdb::MetainferenceBase::calculateNumericalDerivatives ( ActionWithValue a = NULL)
inlineoverridevirtual

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, and PLMD::piv::PIV.

◆ 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]

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

Check if numerical derivatives should be performed.

Reimplemented in PLMD::ActionWithValue.

◆ checkNumericalDerivatives() [2/2]

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

Check if numerical derivatives should be used.

Reimplemented from PLMD::Action.

◆ checkRead()

void PLMD::Action::checkRead ( )
inherited

Check if Action was properly read.

This checks if Action::line is empty. It must be called after a final Action has been initialized

◆ checkUpdate()

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

Check if action should be updated.

◆ cite()

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

Cite a paper see PlumedMain::cite.

◆ clearDependencies()

void PLMD::Action::clearDependencies ( )
inherited

Clear the dependence list for this Action.

◆ clearDerivatives()

void PLMD::ActionWithValue::clearDerivatives ( )
virtualinherited

Clear the derivatives of values wrt parameters.

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

◆ clearInputForces()

void PLMD::ActionWithValue::clearInputForces ( )
inherited

Clear the forces on the values.

◆ clearOptions()

void PLMD::Action::clearOptions ( )
virtualinherited

◆ clearOutputForces()

void PLMD::ActionAtomistic::clearOutputForces ( )
inherited

◆ componentIsNotPeriodic()

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

Set your value component to have no periodicity.

◆ componentIsPeriodic()

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

Set the value to be periodic with a particular domain.

◆ componentsAreNotOptional()

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

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

◆ copyOutput() [1/2]

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

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

Use getPntrToComponent instead.

◆ copyOutput() [2/2]

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

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

Use getPntrToComponent instead.

◆ deactivate()

void PLMD::Action::deactivate ( )
inlinevirtualinherited

Set action to inactive.

◆ difference()

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

Takes the difference taking into account pbc for arg i.

◆ do_regression_zero()

void PLMD::isdb::MetainferenceBase::do_regression_zero ( const std::vector< double > &  mean)
private

◆ doMonteCarlo()

double PLMD::isdb::MetainferenceBase::doMonteCarlo ( const std::vector< double > &  mean)
private

◆ 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 ( const 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.

◆ 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)

◆ get_sigma_mean()

void PLMD::isdb::MetainferenceBase::get_sigma_mean ( const double  weight,
const double  norm,
const double  neff,
const std::vector< double > &  mean 
)
private

◆ get_weights()

void PLMD::isdb::MetainferenceBase::get_weights ( double &  weight,
double &  norm,
double &  neff 
)
private

◆ 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.

◆ getArgument()

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

Returns the value of an argument.

◆ getArguments()

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

Returns an array of pointers to the arguments.

◆ getBox()

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

Get box shape.

◆ getCalcData()

double PLMD::isdb::MetainferenceBase::getCalcData ( const unsigned  index)
inlineprivate

◆ getCharge()

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

Get charge of i-th atom.

◆ getComponent()

int PLMD::ActionWithValue::getComponent ( const std::string &  name) const
privateinherited

Return the index for the component named name.

◆ 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.

◆ getDependencies()

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

Return dependencies.

◆ getDocumentation()

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

◆ getDoScore()

bool PLMD::isdb::MetainferenceBase::getDoScore ( )
inline

◆ getEnergy()

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

Get energy.

◆ getEnergyForceGJ()

void PLMD::isdb::MetainferenceBase::getEnergyForceGJ ( const std::vector< double > &  mean,
const std::vector< double > &  dmean_x,
const std::vector< double > &  dmean_b 
)
private

◆ getEnergyForceGJE()

void PLMD::isdb::MetainferenceBase::getEnergyForceGJE ( const std::vector< double > &  mean,
const std::vector< double > &  dmean_x,
const std::vector< double > &  dmean_b 
)
private

◆ getEnergyForceMIGEN()

void PLMD::isdb::MetainferenceBase::getEnergyForceMIGEN ( const std::vector< double > &  mean,
const std::vector< double > &  dmean_x,
const std::vector< double > &  dmean_b 
)
private

◆ getEnergyForceSP()

void PLMD::isdb::MetainferenceBase::getEnergyForceSP ( const std::vector< double > &  mean,
const std::vector< double > &  dmean_x,
const std::vector< double > &  dmean_b 
)
private

◆ getEnergyForceSPE()

void PLMD::isdb::MetainferenceBase::getEnergyForceSPE ( const std::vector< double > &  mean,
const std::vector< double > &  dmean_x,
const std::vector< double > &  dmean_b 
)
private

◆ getEnergyGJ()

double PLMD::isdb::MetainferenceBase::getEnergyGJ ( const std::vector< double > &  mean,
const std::vector< double > &  sigma,
const double  scale,
const double  offset 
)
private

◆ getEnergyGJE()

double PLMD::isdb::MetainferenceBase::getEnergyGJE ( const std::vector< double > &  mean,
const std::vector< double > &  sigma,
const double  scale,
const double  offset 
)
private

◆ getEnergyMIGEN()

double PLMD::isdb::MetainferenceBase::getEnergyMIGEN ( const std::vector< double > &  mean,
const std::vector< double > &  ftilde,
const std::vector< double > &  sigma,
const double  scale,
const double  offset 
)
private

◆ getEnergySP()

double PLMD::isdb::MetainferenceBase::getEnergySP ( const std::vector< double > &  mean,
const std::vector< double > &  sigma,
const double  scale,
const double  offset 
)
private

◆ getEnergySPE()

double PLMD::isdb::MetainferenceBase::getEnergySPE ( const std::vector< double > &  mean,
const std::vector< double > &  sigma,
const double  scale,
const double  offset 
)
private

◆ getExchangeStep()

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

Check if we are on an exchange step.

◆ getGlobalPosition()

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

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

With direct access to the global atom array.

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

◆ getKeyword()

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

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

◆ getLabel()

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

Returns the label.

◆ getMass()

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

Get mass of i-th atom.

◆ getMetaDer()

double PLMD::isdb::MetainferenceBase::getMetaDer ( const unsigned  index)
inline

◆ getName()

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

Returns the name.

◆ getNarg()

unsigned PLMD::isdb::MetainferenceBase::getNarg ( )
inline

◆ getNumberOfArguments()

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

Returns the number of arguments.

Reimplemented in PLMD::vesselbase::ActionWithAveraging.

◆ getNumberOfAtoms()

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

Get number of available atoms.

◆ getNumberOfComponents()

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

Returns the number of values defined.

◆ getNumberOfDerivatives()

unsigned PLMD::isdb::MetainferenceBase::getNumberOfDerivatives ( )
inlineoverridevirtual

Implements PLMD::ActionWithValue.

◆ getOutputQuantity() [1/2]

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)

◆ getOutputQuantity() [2/2]

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

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

◆ getPbc()

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

Get reference to Pbc.

◆ getPntrToArgument()

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

Return a pointer to specific argument.

◆ getPntrToComponent() [1/2]

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

Return a pointer to the value by name.

◆ getPntrToComponent() [2/2]

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

Return a pointer to the component by index.

◆ getPntrToValue()

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

Get a pointer to the default value.

◆ getPosition()

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

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

◆ 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.

◆ getScore()

double PLMD::isdb::MetainferenceBase::getScore ( )

◆ getStep()

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

Return the present timestep.

◆ getTime()

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

Return the present time.

◆ getTimeStep()

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

Return the timestep.

◆ getTotAtoms()

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

Get total number of atoms, including virtual ones.

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

◆ getUnique()

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

◆ getUniqueLocal()

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

◆ getWstride()

unsigned PLMD::isdb::MetainferenceBase::getWstride ( )
inline

◆ Initialise()

void PLMD::isdb::MetainferenceBase::Initialise ( const unsigned  input)

◆ 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.

◆ lockRequests()

void PLMD::isdb::MetainferenceBase::lockRequests ( )
inlineoverridevirtual

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.

◆ modifyForceOnExtraCV()

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

Get a reference to force on extraCV.

◆ modifyForces()

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

Get a reference to forces array.

◆ modifyGlobalForce()

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

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

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

◆ modifyGlobalPbc()

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

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

◆ modifyGlobalPosition()

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

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

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

◆ modifyGlobalVirial()

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

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

◆ modifyVirial()

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

Get a reference to virial array.

◆ moveScaleOffset()

void PLMD::isdb::MetainferenceBase::moveScaleOffset ( const std::vector< double > &  mean_,
double &  old_energy 
)
private

◆ moveSigmas()

void PLMD::isdb::MetainferenceBase::moveSigmas ( const std::vector< double > &  mean_,
double &  old_energy,
const unsigned  i,
const std::vector< unsigned > &  indices,
bool &  breaknow 
)
private

◆ moveTilde()

void PLMD::isdb::MetainferenceBase::moveTilde ( const std::vector< double > &  mean_,
double &  old_energy 
)
private

◆ 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.

◆ parse()

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

Parse one keyword as generic type.

◆ parseArgumentList() [1/2]

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

Parse a numbered list of arguments.

◆ parseArgumentList() [2/2]

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

Parse a list of arguments.

◆ parseAtomList() [1/2]

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.

◆ parseAtomList() [2/2]

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

Parse a list of atoms without a numbered keyword.

◆ parseFlag()

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

Parse one keyword as boolean flag.

◆ parseNumbered()

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

Parse one numbered keyword as generic type.

◆ parseNumberedVector()

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

Parse a vector with a number.

◆ parseVector()

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

Parse one keyword as std::vector.

◆ pbcApply()

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

Applies PBCs to a seriens of positions or distances.

◆ pbcDistance()

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

Compute the pbc distance between two positions.

◆ prepare()

void PLMD::Action::prepare ( )
virtualinherited

Prepare an Action for calculation This can be used by Action if they need some special preparation before calculation.

Typical case is for collective variables which would like to change their list of requested atoms. By default (if not overridden) does nothing.

Reimplemented in PLMD::isdb::EMMI, PLMD::function::FuncPathMSD, PLMD::generic::Plumed, PLMD::multicolvar::MultiColvarBase, PLMD::generic::Read, PLMD::generic::DumpMassCharge, PLMD::generic::UpdateIf, PLMD::generic::Print, PLMD::GenericMolInfo, PLMD::gridtools::ConvertToFES, PLMD::colvar::Energy, PLMD::colvar::ExtraCV, PLMD::colvar::CoordinationBase, PLMD::function::FuncPathGeneral, PLMD::maze::Optimizer, and PLMD::s2cm::S2ContactModel.

◆ readAtomsFromPDB()

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

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

Reimplemented from PLMD::Action.

◆ registerKeywords()

void PLMD::isdb::MetainferenceBase::registerKeywords ( Keywords keys)
static

◆ replica_averaging()

void PLMD::isdb::MetainferenceBase::replica_averaging ( const double  weight,
const double  norm,
std::vector< double > &  mean,
std::vector< double > &  dmean_b 
)
private

◆ requestArguments()

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

Setup the dependencies.

◆ requestAtoms()

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

Request an array of atoms.

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

◆ requestExtraDependencies()

void PLMD::ActionWithArguments::requestExtraDependencies ( const std::vector< Value * > &  extra)
inherited

◆ retrieveAtoms()

void PLMD::ActionAtomistic::retrieveAtoms ( )
virtualinherited

◆ runFinalJobs()

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

RunFinalJobs This method is called once at the very end of the calculation.

The set of all Actions in run for the final time in forward order.

Reimplemented in PLMD::vesselbase::ActionWithAveraging, PLMD::analysis::AnalysisBase, PLMD::gridtools::ConvertToFES, PLMD::analysis::ReadDissimilarityMatrix, and PLMD::gridtools::GridPrintingBase.

◆ Selector()

void PLMD::isdb::MetainferenceBase::Selector ( )

◆ setArgDerivatives()

void PLMD::isdb::MetainferenceBase::setArgDerivatives ( Value v,
const double &  d 
)
inline

◆ setAtomsDerivatives()

void PLMD::isdb::MetainferenceBase::setAtomsDerivatives ( Value v,
const unsigned  i,
const Vector d 
)
inline

◆ setBoxDerivatives()

void PLMD::isdb::MetainferenceBase::setBoxDerivatives ( Value v,
const Tensor d 
)
inline

◆ setCalcData() [1/2]

void PLMD::isdb::MetainferenceBase::setCalcData ( const std::vector< double > &  data)
inline

◆ setCalcData() [2/2]

void PLMD::isdb::MetainferenceBase::setCalcData ( const unsigned  index,
const double  datum 
)
inline

◆ setDerivatives()

void PLMD::isdb::MetainferenceBase::setDerivatives ( )
inline

◆ setExtraCV()

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

◆ setForcesOnAtoms()

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

Add the forces to the atoms.

◆ setGradientsIfNeeded()

void PLMD::ActionWithValue::setGradientsIfNeeded ( )
inherited

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

◆ setMetaDer()

void PLMD::isdb::MetainferenceBase::setMetaDer ( const unsigned  index,
const double  der 
)
inlineprivate

◆ setNarg()

void PLMD::isdb::MetainferenceBase::setNarg ( const unsigned  input)
inline

◆ setNotPeriodic()

void PLMD::ActionWithValue::setNotPeriodic ( )
inherited

Set your default value to have no periodicity.

◆ setOption()

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

◆ setParameter()

void PLMD::isdb::MetainferenceBase::setParameter ( const double  input)
inline

◆ setParameters()

void PLMD::isdb::MetainferenceBase::setParameters ( const std::vector< double > &  input)
inline

◆ setPeriodic()

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

Set the value to be periodic with a particular domain.

◆ setScore()

void PLMD::isdb::MetainferenceBase::setScore ( const double  score)
inline

◆ 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.

◆ turnOnDerivatives()

void PLMD::isdb::MetainferenceBase::turnOnDerivatives ( )
inlineoverridevirtual

Activate the calculation of derivatives.

Reimplemented from PLMD::ActionWithValue.

◆ unlockRequests()

void PLMD::isdb::MetainferenceBase::unlockRequests ( )
inlineoverridevirtual

Reimplemented from PLMD::ActionAtomistic.

◆ update()

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

◆ 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.

◆ warning()

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

Issue a warning.

◆ writeStatus()

void PLMD::isdb::MetainferenceBase::writeStatus ( )

Member Data Documentation

◆ active

bool PLMD::Action::active
privateinherited

Switch to activate Action on this step.

◆ after

Dependencies PLMD::Action::after
privateinherited

Actions on which this Action depends.

◆ arguments

std::vector<Value*> PLMD::ActionWithArguments::arguments
privateinherited

◆ atoms

Atoms& PLMD::ActionAtomistic::atoms
protectedinherited

◆ average_weights_

std::vector< std::vector <double> > PLMD::isdb::MetainferenceBase::average_weights_
private

◆ calc_data_

std::vector<double> PLMD::isdb::MetainferenceBase::calc_data_
private

◆ charges

std::vector<double> PLMD::ActionAtomistic::charges
privateinherited

◆ chargesWereSet

bool PLMD::ActionAtomistic::chargesWereSet
privateinherited

◆ comm

Communicator& PLMD::Action::comm
inherited

◆ decay_w_

double PLMD::isdb::MetainferenceBase::decay_w_
private

◆ Dftilde_

double PLMD::isdb::MetainferenceBase::Dftilde_
private

◆ do_optsigmamean_

unsigned PLMD::isdb::MetainferenceBase::do_optsigmamean_
private

◆ do_reweight_

bool PLMD::isdb::MetainferenceBase::do_reweight_
private

◆ doCheckPoint

bool PLMD::Action::doCheckPoint
privateinherited

◆ Doffset_

double PLMD::isdb::MetainferenceBase::Doffset_
private

◆ donotforce

bool PLMD::ActionAtomistic::donotforce
privateinherited

◆ donotretrieve

bool PLMD::ActionAtomistic::donotretrieve
privateinherited

◆ dooffset_

bool PLMD::isdb::MetainferenceBase::dooffset_
private

◆ doregres_zero_

bool PLMD::isdb::MetainferenceBase::doregres_zero_
private

◆ doscale_

bool PLMD::isdb::MetainferenceBase::doscale_
private

◆ doscore_

bool PLMD::isdb::MetainferenceBase::doscore_
private

◆ Dscale_

double PLMD::isdb::MetainferenceBase::Dscale_
private

◆ Dsigma_

std::vector<double> PLMD::isdb::MetainferenceBase::Dsigma_
private

◆ energy

double PLMD::ActionAtomistic::energy
privateinherited

◆ extraCV

std::string PLMD::ActionAtomistic::extraCV
privateinherited

◆ files

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

◆ firstTime

bool PLMD::isdb::MetainferenceBase::firstTime
private

◆ firstTimeW

std::vector<bool> PLMD::isdb::MetainferenceBase::firstTimeW
private

◆ forceOnEnergy

double PLMD::ActionAtomistic::forceOnEnergy
privateinherited

◆ forceOnExtraCV

double PLMD::ActionAtomistic::forceOnExtraCV
privateinherited

◆ forces

std::vector<double> PLMD::isdb::MetainferenceBase::forces
private

◆ forcesToApply

std::vector<double> PLMD::isdb::MetainferenceBase::forcesToApply
private

◆ ftilde_

std::vector<double> PLMD::isdb::MetainferenceBase::ftilde_
private

◆ gen_likelihood_

unsigned PLMD::isdb::MetainferenceBase::gen_likelihood_
private

◆ indexes

std::vector<AtomNumber> PLMD::ActionAtomistic::indexes
privateinherited

◆ iselect

unsigned PLMD::isdb::MetainferenceBase::iselect
private

◆ kbt_

double PLMD::isdb::MetainferenceBase::kbt_
private

◆ keywords

const Keywords& PLMD::Action::keywords
inherited

◆ label

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

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

◆ line

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

Directive line.

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

◆ lockRequestArguments

bool PLMD::ActionWithArguments::lockRequestArguments
privateinherited

◆ lockRequestAtoms

bool PLMD::ActionAtomistic::lockRequestAtoms
privateinherited

◆ log

Log& PLMD::Action::log
inherited

Reference to the log stream.

◆ masses

std::vector<double> PLMD::ActionAtomistic::masses
privateinherited

◆ master

bool PLMD::isdb::MetainferenceBase::master
private

◆ MCaccept_

long unsigned PLMD::isdb::MetainferenceBase::MCaccept_
private

◆ MCacceptFT_

long unsigned PLMD::isdb::MetainferenceBase::MCacceptFT_
private

◆ MCacceptScale_

long unsigned PLMD::isdb::MetainferenceBase::MCacceptScale_
private

◆ MCchunksize_

unsigned PLMD::isdb::MetainferenceBase::MCchunksize_
private

◆ MCsteps_

unsigned PLMD::isdb::MetainferenceBase::MCsteps_
private

◆ MCtrial_

long unsigned PLMD::isdb::MetainferenceBase::MCtrial_
private

◆ metader_

std::vector<double> PLMD::isdb::MetainferenceBase::metader_
private

◆ multi_sim_comm

Communicator& PLMD::Action::multi_sim_comm
inherited

◆ N_optimized_step_

unsigned PLMD::isdb::MetainferenceBase::N_optimized_step_
private

◆ name

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

Name of the directive in the plumed.dat file.

◆ narg

unsigned PLMD::isdb::MetainferenceBase::narg
private

◆ noderiv

bool PLMD::ActionWithValue::noderiv
privateinherited

Are we skipping the calculation of the derivatives.

◆ noise_type_

unsigned PLMD::isdb::MetainferenceBase::noise_type_
private

◆ nregres_zero_

int PLMD::isdb::MetainferenceBase::nregres_zero_
private

◆ nrep_

unsigned PLMD::isdb::MetainferenceBase::nrep_
private

◆ nsel_

unsigned PLMD::isdb::MetainferenceBase::nsel_
private

◆ numericalDerivatives

bool PLMD::ActionWithValue::numericalDerivatives
privateinherited

Are we using numerical derivatives to differentiate.

◆ offset_

double PLMD::isdb::MetainferenceBase::offset_
private

◆ offset_max_

double PLMD::isdb::MetainferenceBase::offset_max_
private

◆ offset_min_

double PLMD::isdb::MetainferenceBase::offset_min_
private

◆ offset_mu_

double PLMD::isdb::MetainferenceBase::offset_mu_
private

◆ offset_prior_

unsigned PLMD::isdb::MetainferenceBase::offset_prior_
private

◆ optimized_step_

unsigned PLMD::isdb::MetainferenceBase::optimized_step_
private

◆ options

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

Option that you might have enabled.

◆ optsigmamean_stride_

unsigned PLMD::isdb::MetainferenceBase::optsigmamean_stride_
private

◆ parameters

std::vector<double> PLMD::isdb::MetainferenceBase::parameters
private

◆ pbc

Pbc& PLMD::ActionAtomistic::pbc =*pbc_fwd
privateinherited

◆ pbc_fwd

ForwardDecl<Pbc> PLMD::ActionAtomistic::pbc_fwd
privateinherited

◆ plumed

PlumedMain& PLMD::Action::plumed
inherited

Reference to main plumed object.

◆ positions

std::vector<Vector> PLMD::ActionAtomistic::positions
privateinherited

◆ random

std::vector<Random> PLMD::isdb::MetainferenceBase::random
private

◆ replica_

unsigned PLMD::isdb::MetainferenceBase::replica_
private

◆ replica_index

int PLMD::Action::replica_index
privateinherited

◆ restart

bool PLMD::Action::restart
privateinherited

◆ scale_

double PLMD::isdb::MetainferenceBase::scale_
private

◆ scale_max_

double PLMD::isdb::MetainferenceBase::scale_max_
private

◆ scale_min_

double PLMD::isdb::MetainferenceBase::scale_min_
private

◆ scale_mu_

double PLMD::isdb::MetainferenceBase::scale_mu_
private

◆ scale_prior_

unsigned PLMD::isdb::MetainferenceBase::scale_prior_
private

◆ selector_

std::string PLMD::isdb::MetainferenceBase::selector_
private

◆ sfile_

OFile PLMD::isdb::MetainferenceBase::sfile_
private

◆ sigma_

std::vector<double> PLMD::isdb::MetainferenceBase::sigma_
private

◆ sigma_max_

std::vector<double> PLMD::isdb::MetainferenceBase::sigma_max_
private

◆ sigma_max_est_

std::vector<double> PLMD::isdb::MetainferenceBase::sigma_max_est_
private

◆ sigma_mean2_

std::vector<double> PLMD::isdb::MetainferenceBase::sigma_mean2_
private

◆ sigma_mean2_last_

std::vector< std::vector < std::vector <double> > > PLMD::isdb::MetainferenceBase::sigma_mean2_last_
private

◆ sigma_min_

std::vector<double> PLMD::isdb::MetainferenceBase::sigma_min_
private

◆ sigmamax_opt_done_

bool PLMD::isdb::MetainferenceBase::sigmamax_opt_done_
private

◆ status_file_name_

std::string PLMD::isdb::MetainferenceBase::status_file_name_
private

◆ unique

std::set<AtomNumber> PLMD::ActionAtomistic::unique
privateinherited

unique should be an ordered set since we later create a vector containing the corresponding indexes

◆ unique_local

std::set<AtomNumber> PLMD::ActionAtomistic::unique_local
privateinherited

unique_local should be an ordered set since we later create a vector containing the corresponding indexes

◆ update_from

double PLMD::Action::update_from
privateinherited

Update only after this time.

◆ update_until

double PLMD::Action::update_until
privateinherited

Update only until this time.

◆ valueAccept

Value* PLMD::isdb::MetainferenceBase::valueAccept
private

◆ valueAcceptFT

Value* PLMD::isdb::MetainferenceBase::valueAcceptFT
private

◆ valueAcceptScale

Value* PLMD::isdb::MetainferenceBase::valueAcceptScale
private

◆ valueFtilde

std::vector<Value*> PLMD::isdb::MetainferenceBase::valueFtilde
private

◆ valueOffset

Value* PLMD::isdb::MetainferenceBase::valueOffset
private

◆ values

std::vector<std::unique_ptr<Value> > PLMD::ActionWithValue::values
privateinherited

An array containing the values for this action.

◆ valueScale

Value* PLMD::isdb::MetainferenceBase::valueScale
private

◆ valueScore

Value* PLMD::isdb::MetainferenceBase::valueScore
private

◆ valueSigma

std::vector<Value*> PLMD::isdb::MetainferenceBase::valueSigma
private

◆ valueSigmaMean

std::vector<Value*> PLMD::isdb::MetainferenceBase::valueSigmaMean
private

◆ virial

Tensor PLMD::ActionAtomistic::virial
privateinherited

◆ write_stride_

unsigned PLMD::isdb::MetainferenceBase::write_stride_
private

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