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


Abstract base class for implementing biases the extents the normal Bias.h class to include functions related to the variational approach. More...

#include <VesBias.h>

Inheritance diagram for PLMD::ves::VesBias:
Inheritance graph
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Public Types

typedef std::vector< Action * > Dependencies
 

Public Member Functions

 VesBias (const ActionOptions &ao)
 
 ~VesBias ()
 
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 apply ()
 Apply an Action. More...
 
void applyBiasCutoff (double &, std::vector< double > &) const
 
void applyBiasCutoff (double &, std::vector< double > &, std::vector< double > &) const
 
virtual void beforeUpdate ()
 Before Update. More...
 
bool biasCutoffActive () const
 
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 calculateFromPDB (const PDB &)
 Calculate the action given a pdb file as input. More...
 
virtual void calculateNumericalDerivatives (ActionWithValue *a=NULL)
 Calculate the numerical derivatives N.B. More...
 
virtual void calculateNumericalDerivatives (ActionWithValue *a=NULL)
 Perform calculation using numerical derivatives N.B. More...
 
virtual double calculateReweightFactor () const
 
virtual void checkFieldsAllowed ()
 
virtual bool checkNeedsGradients () const
 Check if the action needs gradient. More...
 
bool checkNumericalDerivatives () const
 Check if numerical derivatives should be used. More...
 
virtual bool checkNumericalDerivatives () const
 Check if numerical derivatives should be performed. More...
 
void checkRead ()
 Check if Action was properly read. More...
 
bool checkUpdate () const
 Check if action should be updated. More...
 
std::string cite (const std::string &s)
 Cite a paper see PlumedMain::cite. More...
 
void clearDependencies ()
 Clear the dependence list for this Action. More...
 
virtual void clearDerivatives ()
 Clear the derivatives of values wrt parameters. More...
 
void clearGradientAndHessian ()
 
void clearInputForces ()
 Clear the forces on the values. More...
 
virtual void clearOptions ()
 
CoeffsVectorCoeffs (const unsigned int coeffs_id=0) const
 
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...
 
bool computeHessian () const
 
ValuecopyOutput (const std::string &name) const
 Return a pointer to the value with name (this is used to retrieve values in other PLMD::Actions) You should NEVER use this routine to refer to the components of your PLMD::Action. More...
 
ValuecopyOutput (const unsigned &n) const
 Return a pointer to the value with this number (this is used to retrieve values in other PLMD::Actions) You should NEVER use this routine to refer to the components of your PLMD::Action. More...
 
virtual void deactivate ()
 Set action to inactive. More...
 
bool diagonalHessian () const
 
double difference (int, double, double) const
 Takes the difference taking into account pbc for arg i. More...
 
void disableBiasFileOutput ()
 
void disableDynamicTargetDistFileOutput ()
 
void disableDynamicTargetDistribution ()
 
void disableFesFileOutput ()
 
void disableFesFileProjOutput ()
 
void disableHessian ()
 
void disableStaticTargetDistFileOutput ()
 
virtual bool doNotCalculateDerivatives () const
 Are we not calculating derivatives. More...
 
bool dynamicTargetDistribution () const
 
void enableBiasFileOutput ()
 
void enableDynamicTargetDistFileOutput ()
 
void enableDynamicTargetDistribution ()
 
void enableFesFileOutput ()
 
void enableFesProjFileOutput ()
 
void enableHessian (const bool diagonal_hessian=true)
 
void enableIterationNumberInFilenames ()
 
void enableMultipleCoeffsSets ()
 
void enableStaticTargetDistFileOutput ()
 
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...
 
bool filenamesIncludeIterationNumber () const
 
FILE * fopen (const char *path, const char *mode)
 Opens a file. 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...
 
double getBeta () const
 
double getBiasCutoffSwitchingFunction (const double, double &) const
 
double getBiasCutoffSwitchingFunction (const double) const
 
double getBiasCutoffValue () const
 
std::string getBiasFileFmt () const
 
std::string getBiasOutputFilename () const
 
size_t getCoeffsIndex (const std::vector< unsigned int > &indices, const unsigned int coeffs_id=0) const
 
std::vector< unsigned int > getCoeffsIndices (const size_t index, const unsigned int coeffs_id=0) const
 
CoeffsVectorgetCoeffsPntr (const unsigned int coeffs_id=0) const
 
std::vector< CoeffsVector * > getCoeffsPntrs () const
 
std::string getCoeffsSetFilenameSuffix (const unsigned int coeffs_id) const
 
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...
 
double getCurrentBiasMaxValue () const
 
std::string getCurrentBiasOutputFilename (const std::string &suffix="") const
 
std::string getCurrentFesOutputFilename (const std::string &suffix="") const
 
std::string getCurrentOutputFilename (const std::string &, const std::string &suffix="") const
 
std::string getCurrentTargetDistOutputFilename (const std::string &suffix="") const
 
const DependenciesgetDependencies () const
 Return dependencies. More...
 
virtual std::string getDocumentation () const
 
bool getExchangeStep () const
 Check if we are on an exchange step. More...
 
std::string getFesFileFmt () const
 
std::string getFesOutputFilename () const
 
CoeffsVectorgetGradientPntr (const unsigned int coeffs_id=0) const
 
std::vector< CoeffsVector * > getGradientPntrs () const
 
std::vector< unsigned int > getGridBins () const
 
std::vector< double > getGridMax () const
 
std::vector< double > getGridMin () const
 
size_t getHessianIndex (const size_t index1, const size_t index2, const unsigned int coeffs_id=0) const
 
CoeffsMatrixgetHessianPntr (const unsigned int coeffs_id=0) const
 
std::vector< CoeffsMatrix * > getHessianPntrs () const
 
unsigned int getIterationCounter () const
 
std::string getIterationFilenameSuffix () const
 
double getKbT () const
 
std::string getKeyword (const std::string &key)
 Just read one of the keywords and return the whole thing as a string. More...
 
const std::string & getLabel () const
 Returns the label. More...
 
const std::string & getName () const
 Returns the name. More...
 
virtual unsigned getNumberOfArguments () const
 Returns the number of arguments. More...
 
int getNumberOfComponents () const
 Returns the number of values defined. More...
 
unsigned getNumberOfDerivatives ()
 
unsigned int getNumberOfProjectionArguments () const
 
unsigned int getNumberOfTargetDistributionPntrs () const
 
OFilegetOFile (const std::string &filename, const bool multi_sim_single_file=false, const bool enforce_backup=true)
 
OptimizergetOptimizerPntr () const
 
double getOutputQuantity (const unsigned j) const
 Get the value of one of the components of the PLMD::Action. More...
 
double getOutputQuantity (const std::string &name) const
 Get the value with a specific name (N.B. if there is no such value this returns zero) More...
 
ValuegetPntrToArgument (const unsigned n)
 Return a pointer to specific argument. More...
 
double getProjection (unsigned i, unsigned j) const
 Get the scalar product between the gradients of two variables. More...
 
std::vector< std::string > getProjectionArgument (unsigned int i) const
 
std::vector< std::vector< std::string > > getProjectionArguments () const
 
bool getRestart () const
 Return true if we are doing a restart. More...
 
long int getStep () const
 Return the present timestep. More...
 
int getStride () const
 Get the stride. More...
 
CoeffsVectorgetTargetDistAveragesPntr (const unsigned int coeffs_id=0) const
 
std::vector< CoeffsVector * > getTargetDistAveragesPntrs () const
 
std::string getTargetDistFileFmt () const
 
std::string getTargetDistOutputFilename () const
 
std::string getTargetDistRestartFileFmt () const
 
std::vector< TargetDistribution * > getTargetDistributionPntrs () const
 
double getTime () const
 Return the present time. More...
 
double getTimeStep () const
 Return the timestep. More...
 
CoeffsVectorGradient (const unsigned int coeffs_id=0) const
 
CoeffsMatrixHessian (const unsigned int coeffs_id=0) const
 
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...
 
bool isActive () const
 Check if action is active. More...
 
bool isBiasFileOutputActive () const
 
bool isDynamicTargetDistFileOutputActive () const
 
bool isFesFileOutputActive () const
 
bool isFesProjFileOutputActive () const
 
bool isOptionOn (const std::string &s) const
 Check if an option is on. More...
 
bool isReweightFactorCalculated () const
 
bool isStaticTargetDistFileOutputActive () const
 
void linkOptimizer (Optimizer *)
 
void lockRequests ()
 
virtual void lockRequests ()
 
size_t numberOfCoeffs (const unsigned int coeffs_id=0) const
 
unsigned int numberOfCoeffsSets () const
 
virtual bool onStep () const
 Check if the action is active on this step. More...
 
bool optimizeCoeffs () const
 
template<class T >
void parse (const std::string &key, T &t)
 Parse one keyword as generic type. More...
 
void parseArgumentList (const std::string &key, std::vector< Value *> &args)
 Parse a list of arguments. More...
 
bool parseArgumentList (const std::string &key, int i, std::vector< Value *> &args)
 Parse a numbered list of arguments. More...
 
void parseFlag (const std::string &key, bool &t)
 Parse one keyword as boolean flag. More...
 
template<class T >
bool parseNumbered (const std::string &key, const int no, T &t)
 Parse one numbered keyword as generic type. More...
 
template<class T >
bool parseNumberedVector (const std::string &key, const int no, std::vector< T > &t)
 Parse a vector with a number. More...
 
template<class T >
void parseVector (const std::string &key, std::vector< T > &t)
 Parse one keyword as std::vector. More...
 
virtual void prepare ()
 Prepare an Action for calculation This can be used by Action if they need some special preparation before calculation. More...
 
virtual void readAtomsFromPDB (const PDB &)
 This is overwritten in ActionAtomistic so that we can read the atoms from the pdb input file rather than taking them from the MD code. More...
 
void requestArguments (const std::vector< Value *> &arg)
 Setup the dependencies. More...
 
virtual void resetBiasFileOutput ()
 
virtual void resetFesFileOutput ()
 
virtual void resetFesProjFileOutput ()
 
virtual void resetTargetDistFileOutput ()
 
virtual void resetTargetDistProjFileOutput ()
 
virtual void restartTargetDistributions ()
 
virtual void runFinalJobs ()
 RunFinalJobs This method is called once at the very end of the calculation. More...
 
void setCurrentBiasMaxValue (const double max_value)
 
void setGradientsIfNeeded ()
 Calculate the gradients and store them for all the values (need for projections) More...
 
void setGridBins (const std::vector< unsigned int > &)
 
void setGridBins (const unsigned int)
 
void setGridMax (const std::vector< double > &)
 
void setGridMin (const std::vector< double > &)
 
void setNotPeriodic ()
 Set your default value to have no periodicity. More...
 
virtual void setOption (const std::string &s)
 
void setPeriodic (const std::string &min, const std::string &max)
 Set the value to be periodic with a particular domain. More...
 
void setStride (const int &n)
 Set the value of the stride. More...
 
void setupBiasCutoff (const double, const double)
 
virtual void setupBiasFileOutput ()
 
virtual void setupFesFileOutput ()
 
virtual void setupFesProjFileOutput ()
 
virtual void setupTargetDistFileOutput ()
 
virtual void setupTargetDistProjFileOutput ()
 
void setValue (Value *, double)
 Set the value. More...
 
CoeffsVectorTargetDistAverages (const unsigned int coeffs_id=0) const
 
size_t totalNumberOfCoeffs () const
 
virtual void turnOnDerivatives ()
 Activate the calculation of derivatives. More...
 
void unlockRequests ()
 
virtual void unlockRequests ()
 
virtual void update ()
 Update. More...
 
void updateGradientAndHessian (const bool)
 
void updateReweightFactor ()
 
virtual void updateTargetDistributions ()
 
bool useMultipleWalkers () const
 
void useNumericalDerivatives ()
 This forces the class to use numerical derivatives. More...
 
void warning (const std::string &msg)
 Issue a warning. More...
 
virtual void writeBiasToFile ()
 
virtual void writeFesProjToFile ()
 
virtual void writeFesToFile ()
 
virtual void writeTargetDistProjToFile ()
 
virtual void writeTargetDistToFile ()
 

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 &)
 
static void useBiasCutoffKeywords (Keywords &)
 
static void useCustomisableComponents (Keywords &keys)
 The components in the action will depend on the user. More...
 
static void useGridBinKeywords (Keywords &)
 
static void useGridLimitsKeywords (Keywords &)
 
static void useInitialCoeffsKeywords (Keywords &)
 
static void useMultipleTargetDistributionKeywords (Keywords &)
 
static void useProjectionArgKeywords (Keywords &)
 
static void useReweightFactorKeywords (Keywords &)
 
static void useTargetDistributionKeywords (Keywords &)
 

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 addCoeffsSet (const std::vector< std::string > &, const std::vector< unsigned int > &)
 
void addCoeffsSet (std::vector< Value *> &, std::vector< BasisFunctions *> &)
 
void addCoeffsSet (CoeffsVector *)
 
void addToSampledAverages (const std::vector< double > &, const unsigned int c_id=0)
 
void checkThatTemperatureIsGiven ()
 
void clearCoeffsPntrsVector ()
 
void expandArgKeywordInPDB (PDB &pdb)
 This changes the arg keyword in the pdb file. More...
 
std::string getCoeffsSetLabelString (const std::string &, const unsigned int coeffs_id=0) const
 
ValuegetPntrToComponent (int i)
 Return a pointer to the component by index. More...
 
ValuegetPntrToComponent (const std::string &name)
 Return a pointer to the value by name. More...
 
ValuegetPntrToValue ()
 Get a pointer to the default value. More...
 
template<class T >
bool parseMultipleValues (const std::string &, std::vector< T > &, unsigned int)
 
template<class T >
bool parseMultipleValues (const std::string &, std::vector< T > &, unsigned int, const T &)
 
bool readCoeffsFromFiles ()
 
void setBias (double bias)
 set the value of the bias More...
 
void setOutputForce (int i, double f)
 set the force from the bias on argument i, this automatically set the partial derivative of the bias with respect to i to -f More...
 
void setTargetDistAverages (const std::vector< double > &, const unsigned int coeffs_id=0)
 
void setTargetDistAverages (const CoeffsVector &, const unsigned int coeffs_id=0)
 
void setTargetDistAveragesToZero (const unsigned int coeffs_id=0)
 
void setValue (const double &d)
 Set the default value (the one without name) More...
 

Private Member Functions

std::vector< double > computeCovarianceFromAverages (const unsigned int) const
 
void initializeCoeffs (CoeffsVector *)
 
void multiSimSumAverages (const unsigned int, const double walker_weight=1.0)
 

Private Attributes

std::vector< unsigned int > aver_counters
 
double bias_current_max_value
 
bool bias_cutoff_active_
 
FermiSwitchingFunctionbias_cutoff_swfunc_pntr_
 
double bias_cutoff_value_
 
std::string bias_file_fmt_
 
std::string bias_filename_
 
bool bias_fileoutput_active_
 
bool calc_reweightfactor_
 
std::vector< std::string > coeffs_fnames
 
std::string coeffs_id_prefix_
 
std::vector< CoeffsVector * > coeffs_pntrs_
 
bool compute_hessian_
 
bool diagonal_hessian_
 
bool dynamic_targetdist_
 
bool dynamic_targetdist_fileoutput_active_
 
std::string fes_file_fmt_
 
std::string fes_filename_
 
bool fes_fileoutput_active_
 
bool fesproj_fileoutput_active_
 
bool filenames_have_iteration_number_
 
std::vector< CoeffsVector * > gradient_pntrs_
 
std::vector< unsigned int > grid_bins_
 
std::vector< double > grid_max_
 
std::vector< double > grid_min_
 
std::vector< CoeffsMatrix * > hessian_pntrs_
 
double kbt_
 
size_t ncoeffs_total_
 
unsigned int ncoeffssets_
 
bool optimize_coeffs_
 
Optimizeroptimizer_pntr_
 
std::vector< std::vector< std::string > > projection_args_
 
std::vector< std::vector< double > > sampled_averages
 
std::vector< std::vector< double > > sampled_cross_averages
 
bool static_targetdist_fileoutput_active_
 
std::string targetdist_averages_filename_
 
std::vector< CoeffsVector * > targetdist_averages_pntrs_
 
std::string targetdist_file_fmt_
 
std::string targetdist_filename_
 
std::vector< TargetDistribution * > targetdist_pntrs_
 
std::string targetdist_restart_file_fmt_
 
bool use_multiple_coeffssets_
 

Detailed Description


Abstract base class for implementing biases the extents the normal Bias.h class to include functions related to the variational approach.

Member Typedef Documentation

◆ Dependencies

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

Constructor & Destructor Documentation

◆ VesBias()

PLMD::ves::VesBias::VesBias ( const ActionOptions ao)
explicit

◆ ~VesBias()

PLMD::ves::VesBias::~VesBias ( )

Member Function Documentation

◆ activate()

void PLMD::Action::activate ( )
virtualinherited

Set action to active.

◆ addCoeffsSet() [1/3]

void PLMD::ves::VesBias::addCoeffsSet ( const std::vector< std::string > &  dimension_labels,
const std::vector< unsigned int > &  indices_shape 
)
protected

◆ addCoeffsSet() [2/3]

void PLMD::ves::VesBias::addCoeffsSet ( std::vector< Value *> &  args,
std::vector< BasisFunctions *> &  basisf 
)
protected

◆ addCoeffsSet() [3/3]

void PLMD::ves::VesBias::addCoeffsSet ( CoeffsVector coeffs_pntr_in)
protected

◆ 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)

◆ addToSampledAverages()

void PLMD::ves::VesBias::addToSampledAverages ( const std::vector< double > &  values,
const unsigned int  c_id = 0 
)
protected

◆ 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.

◆ apply()

void PLMD::ves::VesBias::apply ( )
virtual

Apply an Action.

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

Reimplemented from PLMD::bias::Bias.

◆ applyBiasCutoff() [1/2]

void PLMD::ves::VesBias::applyBiasCutoff ( double &  bias,
std::vector< double > &  forces 
) const
inline

◆ applyBiasCutoff() [2/2]

void PLMD::ves::VesBias::applyBiasCutoff ( double &  bias,
std::vector< double > &  forces,
std::vector< double > &  coeffsderivs_values 
) const
inline

◆ 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.

◆ biasCutoffActive()

bool PLMD::ves::VesBias::biasCutoffActive ( ) const
inline

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

◆ 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() [1/2]

void PLMD::ActionWithArguments::calculateNumericalDerivatives ( ActionWithValue a = NULL)
virtualinherited

Calculate the numerical derivatives 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::Action.

Reimplemented in PLMD::isdb::MetainferenceBase, PLMD::mapping::PCAVars, PLMD::analysis::AnalysisBase, PLMD::vesselbase::ActionWithAveraging, and PLMD::mapping::Mapping.

◆ calculateNumericalDerivatives() [2/2]

void PLMD::Action::calculateNumericalDerivatives ( ActionWithValue a = NULL)
virtualinherited

◆ calculateReweightFactor()

double PLMD::ves::VesBias::calculateReweightFactor ( ) const
virtual

Reimplemented in PLMD::ves::VesLinearExpansion.

◆ checkFieldsAllowed()

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

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

◆ checkNeedsGradients()

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

Check if the action needs gradient.

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

◆ checkNumericalDerivatives() [1/2]

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

Check if numerical derivatives should be used.

Reimplemented from PLMD::Action.

◆ checkNumericalDerivatives() [2/2]

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

Check if numerical derivatives should be performed.

Reimplemented in PLMD::ActionWithValue.

◆ checkRead()

void PLMD::Action::checkRead ( )
inherited

Check if Action was properly read.

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

◆ checkThatTemperatureIsGiven()

void PLMD::ves::VesBias::checkThatTemperatureIsGiven ( )
protected

◆ 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.

◆ clearCoeffsPntrsVector()

void PLMD::ves::VesBias::clearCoeffsPntrsVector ( )
inlineprotected

◆ 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.

◆ clearGradientAndHessian()

void PLMD::ves::VesBias::clearGradientAndHessian ( )
inline

◆ clearInputForces()

void PLMD::ActionWithValue::clearInputForces ( )
inherited

Clear the forces on the values.

◆ clearOptions()

void PLMD::Action::clearOptions ( )
virtualinherited

◆ Coeffs()

CoeffsVector& PLMD::ves::VesBias::Coeffs ( const unsigned int  coeffs_id = 0) const
inline

◆ 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.

◆ computeCovarianceFromAverages()

std::vector< double > PLMD::ves::VesBias::computeCovarianceFromAverages ( const unsigned int  c_id) const
inlineprivate

◆ computeHessian()

bool PLMD::ves::VesBias::computeHessian ( ) const
inline

◆ 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.

◆ diagonalHessian()

bool PLMD::ves::VesBias::diagonalHessian ( ) const
inline

◆ difference()

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

Takes the difference taking into account pbc for arg i.

◆ disableBiasFileOutput()

void PLMD::ves::VesBias::disableBiasFileOutput ( )
inline

◆ disableDynamicTargetDistFileOutput()

void PLMD::ves::VesBias::disableDynamicTargetDistFileOutput ( )
inline

◆ disableDynamicTargetDistribution()

void PLMD::ves::VesBias::disableDynamicTargetDistribution ( )
inline

◆ disableFesFileOutput()

void PLMD::ves::VesBias::disableFesFileOutput ( )
inline

◆ disableFesFileProjOutput()

void PLMD::ves::VesBias::disableFesFileProjOutput ( )
inline

◆ disableHessian()

void PLMD::ves::VesBias::disableHessian ( )

◆ disableStaticTargetDistFileOutput()

void PLMD::ves::VesBias::disableStaticTargetDistFileOutput ( )
inline

◆ doNotCalculateDerivatives()

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

Are we not calculating derivatives.

Reimplemented in PLMD::multicolvar::MultiColvarBase.

◆ dynamicTargetDistribution()

bool PLMD::ves::VesBias::dynamicTargetDistribution ( ) const
inline

◆ enableBiasFileOutput()

void PLMD::ves::VesBias::enableBiasFileOutput ( )
inline

◆ enableDynamicTargetDistFileOutput()

void PLMD::ves::VesBias::enableDynamicTargetDistFileOutput ( )
inline

◆ enableDynamicTargetDistribution()

void PLMD::ves::VesBias::enableDynamicTargetDistribution ( )
inline

◆ enableFesFileOutput()

void PLMD::ves::VesBias::enableFesFileOutput ( )
inline

◆ enableFesProjFileOutput()

void PLMD::ves::VesBias::enableFesProjFileOutput ( )
inline

◆ enableHessian()

void PLMD::ves::VesBias::enableHessian ( const bool  diagonal_hessian = true)

◆ enableIterationNumberInFilenames()

void PLMD::ves::VesBias::enableIterationNumberInFilenames ( )
inline

◆ enableMultipleCoeffsSets()

void PLMD::ves::VesBias::enableMultipleCoeffsSets ( )
inline

◆ enableStaticTargetDistFileOutput()

void PLMD::ves::VesBias::enableStaticTargetDistFileOutput ( )
inline

◆ error()

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

Crash calculation and print documentation.

◆ exists()

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

Check if a value with a particular name is present.

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

◆ exit()

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

Exit with error code c.

◆ expandArgKeywordInPDB()

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

This changes the arg keyword in the pdb file.

◆ fclose()

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

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

◆ fflush()

void PLMD::Action::fflush ( )
inherited

Tell to the Action to flush open files.

◆ filenamesIncludeIterationNumber()

bool PLMD::ves::VesBias::filenamesIncludeIterationNumber ( ) const
inline

◆ 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)

◆ 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.

◆ getBeta()

double PLMD::ves::VesBias::getBeta ( ) const
inline

◆ getBiasCutoffSwitchingFunction() [1/2]

double PLMD::ves::VesBias::getBiasCutoffSwitchingFunction ( const double  bias,
double &  deriv_factor 
) const

◆ getBiasCutoffSwitchingFunction() [2/2]

double PLMD::ves::VesBias::getBiasCutoffSwitchingFunction ( const double  bias) const
inline

◆ getBiasCutoffValue()

double PLMD::ves::VesBias::getBiasCutoffValue ( ) const
inline

◆ getBiasFileFmt()

std::string PLMD::ves::VesBias::getBiasFileFmt ( ) const
inline

◆ getBiasOutputFilename()

std::string PLMD::ves::VesBias::getBiasOutputFilename ( ) const
inline

◆ getCoeffsIndex()

size_t PLMD::ves::VesBias::getCoeffsIndex ( const std::vector< unsigned int > &  indices,
const unsigned int  coeffs_id = 0 
) const
inline

◆ getCoeffsIndices()

std::vector< unsigned int > PLMD::ves::VesBias::getCoeffsIndices ( const size_t  index,
const unsigned int  coeffs_id = 0 
) const
inline

◆ getCoeffsPntr()

CoeffsVector* PLMD::ves::VesBias::getCoeffsPntr ( const unsigned int  coeffs_id = 0) const
inline

◆ getCoeffsPntrs()

std::vector<CoeffsVector*> PLMD::ves::VesBias::getCoeffsPntrs ( ) const
inline

◆ getCoeffsSetFilenameSuffix()

std::string PLMD::ves::VesBias::getCoeffsSetFilenameSuffix ( const unsigned int  coeffs_id) const

◆ getCoeffsSetLabelString()

std::string PLMD::ves::VesBias::getCoeffsSetLabelString ( const std::string &  type,
const unsigned int  coeffs_id = 0 
) const
protected

◆ 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.

◆ getCurrentBiasMaxValue()

double PLMD::ves::VesBias::getCurrentBiasMaxValue ( ) const
inline

◆ getCurrentBiasOutputFilename()

std::string PLMD::ves::VesBias::getCurrentBiasOutputFilename ( const std::string &  suffix = "") const
inline

◆ getCurrentFesOutputFilename()

std::string PLMD::ves::VesBias::getCurrentFesOutputFilename ( const std::string &  suffix = "") const
inline

◆ getCurrentOutputFilename()

std::string PLMD::ves::VesBias::getCurrentOutputFilename ( const std::string &  base_filename,
const std::string &  suffix = "" 
) const

◆ getCurrentTargetDistOutputFilename()

std::string PLMD::ves::VesBias::getCurrentTargetDistOutputFilename ( const std::string &  suffix = "") const

◆ getDependencies()

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

Return dependencies.

◆ getDocumentation()

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

◆ getExchangeStep()

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

Check if we are on an exchange step.

◆ getFesFileFmt()

std::string PLMD::ves::VesBias::getFesFileFmt ( ) const
inline

◆ getFesOutputFilename()

std::string PLMD::ves::VesBias::getFesOutputFilename ( ) const
inline

◆ getGradientPntr()

CoeffsVector* PLMD::ves::VesBias::getGradientPntr ( const unsigned int  coeffs_id = 0) const
inline

◆ getGradientPntrs()

std::vector<CoeffsVector*> PLMD::ves::VesBias::getGradientPntrs ( ) const
inline

◆ getGridBins()

std::vector<unsigned int> PLMD::ves::VesBias::getGridBins ( ) const
inline

◆ getGridMax()

std::vector<double> PLMD::ves::VesBias::getGridMax ( ) const
inline

◆ getGridMin()

std::vector<double> PLMD::ves::VesBias::getGridMin ( ) const
inline

◆ getHessianIndex()

size_t PLMD::ves::VesBias::getHessianIndex ( const size_t  index1,
const size_t  index2,
const unsigned int  coeffs_id = 0 
) const
inline

◆ getHessianPntr()

CoeffsMatrix* PLMD::ves::VesBias::getHessianPntr ( const unsigned int  coeffs_id = 0) const
inline

◆ getHessianPntrs()

std::vector<CoeffsMatrix*> PLMD::ves::VesBias::getHessianPntrs ( ) const
inline

◆ getIterationCounter()

unsigned int PLMD::ves::VesBias::getIterationCounter ( ) const

◆ getIterationFilenameSuffix()

std::string PLMD::ves::VesBias::getIterationFilenameSuffix ( ) const

◆ getKbT()

double PLMD::ves::VesBias::getKbT ( ) const
inline

◆ getKeyword()

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

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

◆ getLabel()

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

Returns the label.

◆ getName()

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

Returns the name.

◆ getNumberOfArguments()

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

Returns the number of arguments.

Reimplemented in PLMD::vesselbase::ActionWithAveraging.

◆ getNumberOfComponents()

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

Returns the number of values defined.

◆ getNumberOfDerivatives()

unsigned PLMD::bias::Bias::getNumberOfDerivatives ( )
inlinevirtualinherited

Implements PLMD::ActionWithValue.

◆ getNumberOfProjectionArguments()

unsigned int PLMD::ves::VesBias::getNumberOfProjectionArguments ( ) const
inline

◆ getNumberOfTargetDistributionPntrs()

unsigned int PLMD::ves::VesBias::getNumberOfTargetDistributionPntrs ( ) const
inline

◆ getOFile()

OFile * PLMD::ves::VesBias::getOFile ( const std::string &  filename,
const bool  multi_sim_single_file = false,
const bool  enforce_backup = true 
)

◆ getOptimizerPntr()

Optimizer* PLMD::ves::VesBias::getOptimizerPntr ( ) const
inline

◆ getOutputQuantity() [1/2]

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

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

◆ getOutputQuantity() [2/2]

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

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

◆ getPntrToArgument()

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

Return a pointer to specific argument.

◆ getPntrToComponent() [1/2]

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

Return a pointer to the component by index.

◆ getPntrToComponent() [2/2]

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

Return a pointer to the value by name.

◆ getPntrToValue()

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

Get a pointer to the default value.

◆ getProjection()

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

Get the scalar product between the gradients of two variables.

◆ getProjectionArgument()

std::vector<std::string> PLMD::ves::VesBias::getProjectionArgument ( unsigned int  i) const
inline

◆ getProjectionArguments()

std::vector< std::vector<std::string> > PLMD::ves::VesBias::getProjectionArguments ( ) const
inline

◆ getRestart()

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

Return true if we are doing a restart.

◆ getStep()

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

Return the present timestep.

◆ getStride()

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

Get the stride.

◆ getTargetDistAveragesPntr()

CoeffsVector* PLMD::ves::VesBias::getTargetDistAveragesPntr ( const unsigned int  coeffs_id = 0) const
inline

◆ getTargetDistAveragesPntrs()

std::vector<CoeffsVector*> PLMD::ves::VesBias::getTargetDistAveragesPntrs ( ) const
inline

◆ getTargetDistFileFmt()

std::string PLMD::ves::VesBias::getTargetDistFileFmt ( ) const
inline

◆ getTargetDistOutputFilename()

std::string PLMD::ves::VesBias::getTargetDistOutputFilename ( ) const
inline

◆ getTargetDistRestartFileFmt()

std::string PLMD::ves::VesBias::getTargetDistRestartFileFmt ( ) const
inline

◆ getTargetDistributionPntrs()

std::vector<TargetDistribution*> PLMD::ves::VesBias::getTargetDistributionPntrs ( ) const
inline

◆ getTime()

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

Return the present time.

◆ getTimeStep()

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

Return the timestep.

◆ Gradient()

CoeffsVector& PLMD::ves::VesBias::Gradient ( const unsigned int  coeffs_id = 0) const
inline

◆ Hessian()

CoeffsMatrix& PLMD::ves::VesBias::Hessian ( const unsigned int  coeffs_id = 0) const
inline

◆ initializeCoeffs()

void PLMD::ves::VesBias::initializeCoeffs ( CoeffsVector coeffs_pntr_in)
private

◆ 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.

◆ isActive()

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

Check if action is active.

◆ isBiasFileOutputActive()

bool PLMD::ves::VesBias::isBiasFileOutputActive ( ) const
inline

◆ isDynamicTargetDistFileOutputActive()

bool PLMD::ves::VesBias::isDynamicTargetDistFileOutputActive ( ) const
inline

◆ isFesFileOutputActive()

bool PLMD::ves::VesBias::isFesFileOutputActive ( ) const
inline

◆ isFesProjFileOutputActive()

bool PLMD::ves::VesBias::isFesProjFileOutputActive ( ) const
inline

◆ isOptionOn()

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

Check if an option is on.

◆ isReweightFactorCalculated()

bool PLMD::ves::VesBias::isReweightFactorCalculated ( ) const
inline

◆ isStaticTargetDistFileOutputActive()

bool PLMD::ves::VesBias::isStaticTargetDistFileOutputActive ( ) const
inline

◆ linkOptimizer()

void PLMD::ves::VesBias::linkOptimizer ( Optimizer optimizer_pntr_in)

◆ lockRequests() [1/2]

void PLMD::ActionWithArguments::lockRequests ( )
inlinevirtualinherited

◆ lockRequests() [2/2]

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

◆ multiSimSumAverages()

void PLMD::ves::VesBias::multiSimSumAverages ( const unsigned int  c_id,
const double  walker_weight = 1.0 
)
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.

◆ numberOfCoeffs()

size_t PLMD::ves::VesBias::numberOfCoeffs ( const unsigned int  coeffs_id = 0) const
inline

◆ numberOfCoeffsSets()

unsigned int PLMD::ves::VesBias::numberOfCoeffsSets ( ) const
inline

◆ onStep()

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

Check if the action is active on this step.

Reimplemented in PLMD::gridtools::ConvertToFES.

◆ optimizeCoeffs()

bool PLMD::ves::VesBias::optimizeCoeffs ( ) const
inline

◆ parse()

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

Parse one keyword as generic type.

◆ parseArgumentList() [1/2]

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

Parse a list of arguments.

◆ parseArgumentList() [2/2]

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

Parse a numbered list of arguments.

◆ parseFlag()

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

Parse one keyword as boolean flag.

◆ parseMultipleValues() [1/2]

template<class T >
bool PLMD::ves::VesBias::parseMultipleValues ( const std::string &  keyword,
std::vector< T > &  values,
unsigned int  nvalues 
)
protected

◆ parseMultipleValues() [2/2]

template<class T >
bool PLMD::ves::VesBias::parseMultipleValues ( const std::string &  keyword,
std::vector< T > &  values,
unsigned int  nvalues,
const T &  default_value 
)
protected

◆ 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.

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

◆ readAtomsFromPDB()

virtual void PLMD::Action::readAtomsFromPDB ( const PDB )
inlinevirtualinherited

This is overwritten in ActionAtomistic so that we can read the atoms from the pdb input file rather than taking them from the MD code.

Reimplemented in PLMD::ActionAtomistic.

◆ readCoeffsFromFiles()

bool PLMD::ves::VesBias::readCoeffsFromFiles ( )
protected

◆ registerKeywords()

void PLMD::ves::VesBias::registerKeywords ( Keywords keys)
static

◆ requestArguments()

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

Setup the dependencies.

◆ resetBiasFileOutput()

virtual void PLMD::ves::VesBias::resetBiasFileOutput ( )
inlinevirtual

Reimplemented in PLMD::ves::VesLinearExpansion.

◆ resetFesFileOutput()

virtual void PLMD::ves::VesBias::resetFesFileOutput ( )
inlinevirtual

Reimplemented in PLMD::ves::VesLinearExpansion.

◆ resetFesProjFileOutput()

virtual void PLMD::ves::VesBias::resetFesProjFileOutput ( )
inlinevirtual

◆ resetTargetDistFileOutput()

virtual void PLMD::ves::VesBias::resetTargetDistFileOutput ( )
inlinevirtual

◆ resetTargetDistProjFileOutput()

virtual void PLMD::ves::VesBias::resetTargetDistProjFileOutput ( )
inlinevirtual

◆ restartTargetDistributions()

virtual void PLMD::ves::VesBias::restartTargetDistributions ( )
inlinevirtual

Reimplemented in PLMD::ves::VesLinearExpansion.

◆ 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.

◆ setBias()

void PLMD::bias::Bias::setBias ( double  bias)
inlineprotectedinherited

set the value of the bias

◆ setCurrentBiasMaxValue()

void PLMD::ves::VesBias::setCurrentBiasMaxValue ( const double  max_value)
inline

◆ setGradientsIfNeeded()

void PLMD::ActionWithValue::setGradientsIfNeeded ( )
inherited

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

◆ setGridBins() [1/2]

void PLMD::ves::VesBias::setGridBins ( const std::vector< unsigned int > &  grid_bins_in)

◆ setGridBins() [2/2]

void PLMD::ves::VesBias::setGridBins ( const unsigned int  nbins)

◆ setGridMax()

void PLMD::ves::VesBias::setGridMax ( const std::vector< double > &  grid_max_in)

◆ setGridMin()

void PLMD::ves::VesBias::setGridMin ( const std::vector< double > &  grid_min_in)

◆ setNotPeriodic()

void PLMD::ActionWithValue::setNotPeriodic ( )
inherited

Set your default value to have no periodicity.

◆ setOption()

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

◆ setOutputForce()

void PLMD::bias::Bias::setOutputForce ( int  i,
double  f 
)
inlineprotectedinherited

set the force from the bias on argument i, this automatically set the partial derivative of the bias with respect to i to -f

◆ setPeriodic()

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

Set the value to be periodic with a particular domain.

◆ setStride()

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

Set the value of the stride.

◆ setTargetDistAverages() [1/2]

void PLMD::ves::VesBias::setTargetDistAverages ( const std::vector< double > &  coeffderivs_aver_ps,
const unsigned int  coeffs_id = 0 
)
protected

◆ setTargetDistAverages() [2/2]

void PLMD::ves::VesBias::setTargetDistAverages ( const CoeffsVector coeffderivs_aver_ps,
const unsigned int  coeffs_id = 0 
)
protected

◆ setTargetDistAveragesToZero()

void PLMD::ves::VesBias::setTargetDistAveragesToZero ( const unsigned int  coeffs_id = 0)
protected

◆ setupBiasCutoff()

void PLMD::ves::VesBias::setupBiasCutoff ( const double  bias_cutoff_value,
const double  fermi_lambda 
)

◆ setupBiasFileOutput()

virtual void PLMD::ves::VesBias::setupBiasFileOutput ( )
inlinevirtual

Reimplemented in PLMD::ves::VesLinearExpansion.

◆ setupFesFileOutput()

virtual void PLMD::ves::VesBias::setupFesFileOutput ( )
inlinevirtual

Reimplemented in PLMD::ves::VesLinearExpansion.

◆ setupFesProjFileOutput()

virtual void PLMD::ves::VesBias::setupFesProjFileOutput ( )
inlinevirtual

Reimplemented in PLMD::ves::VesLinearExpansion.

◆ setupTargetDistFileOutput()

virtual void PLMD::ves::VesBias::setupTargetDistFileOutput ( )
inlinevirtual

◆ setupTargetDistProjFileOutput()

virtual void PLMD::ves::VesBias::setupTargetDistProjFileOutput ( )
inlinevirtual

◆ 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.

◆ TargetDistAverages()

CoeffsVector& PLMD::ves::VesBias::TargetDistAverages ( const unsigned int  coeffs_id = 0) const
inline

◆ totalNumberOfCoeffs()

size_t PLMD::ves::VesBias::totalNumberOfCoeffs ( ) const
inline

◆ turnOnDerivatives()

void PLMD::ActionWithValue::turnOnDerivatives ( )
virtualinherited

◆ unlockRequests() [1/2]

void PLMD::ActionWithArguments::unlockRequests ( )
inlinevirtualinherited

◆ unlockRequests() [2/2]

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

◆ update()

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

◆ updateGradientAndHessian()

void PLMD::ves::VesBias::updateGradientAndHessian ( const bool  use_mwalkers_mpi)

◆ updateReweightFactor()

void PLMD::ves::VesBias::updateReweightFactor ( )

◆ updateTargetDistributions()

virtual void PLMD::ves::VesBias::updateTargetDistributions ( )
inlinevirtual

Reimplemented in PLMD::ves::VesLinearExpansion.

◆ useBiasCutoffKeywords()

void PLMD::ves::VesBias::useBiasCutoffKeywords ( Keywords keys)
static

◆ useCustomisableComponents()

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

The components in the action will depend on the user.

◆ useGridBinKeywords()

void PLMD::ves::VesBias::useGridBinKeywords ( Keywords keys)
static

◆ useGridLimitsKeywords()

void PLMD::ves::VesBias::useGridLimitsKeywords ( Keywords keys)
static

◆ useInitialCoeffsKeywords()

void PLMD::ves::VesBias::useInitialCoeffsKeywords ( Keywords keys)
static

◆ useMultipleTargetDistributionKeywords()

void PLMD::ves::VesBias::useMultipleTargetDistributionKeywords ( Keywords keys)
static

◆ useMultipleWalkers()

bool PLMD::ves::VesBias::useMultipleWalkers ( ) const

◆ useNumericalDerivatives()

void PLMD::ActionWithValue::useNumericalDerivatives ( )
inlineinherited

This forces the class to use numerical derivatives.

◆ useProjectionArgKeywords()

void PLMD::ves::VesBias::useProjectionArgKeywords ( Keywords keys)
static

◆ useReweightFactorKeywords()

void PLMD::ves::VesBias::useReweightFactorKeywords ( Keywords keys)
static

◆ useTargetDistributionKeywords()

void PLMD::ves::VesBias::useTargetDistributionKeywords ( Keywords keys)
static

◆ warning()

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

Issue a warning.

◆ writeBiasToFile()

virtual void PLMD::ves::VesBias::writeBiasToFile ( )
inlinevirtual

Reimplemented in PLMD::ves::VesLinearExpansion.

◆ writeFesProjToFile()

virtual void PLMD::ves::VesBias::writeFesProjToFile ( )
inlinevirtual

Reimplemented in PLMD::ves::VesLinearExpansion.

◆ writeFesToFile()

virtual void PLMD::ves::VesBias::writeFesToFile ( )
inlinevirtual

Reimplemented in PLMD::ves::VesLinearExpansion.

◆ writeTargetDistProjToFile()

virtual void PLMD::ves::VesBias::writeTargetDistProjToFile ( )
inlinevirtual

Reimplemented in PLMD::ves::VesLinearExpansion.

◆ writeTargetDistToFile()

virtual void PLMD::ves::VesBias::writeTargetDistToFile ( )
inlinevirtual

Reimplemented in PLMD::ves::VesLinearExpansion.

Member Data Documentation

◆ aver_counters

std::vector<unsigned int> PLMD::ves::VesBias::aver_counters
private

◆ bias_current_max_value

double PLMD::ves::VesBias::bias_current_max_value
private

◆ bias_cutoff_active_

bool PLMD::ves::VesBias::bias_cutoff_active_
private

◆ bias_cutoff_swfunc_pntr_

FermiSwitchingFunction* PLMD::ves::VesBias::bias_cutoff_swfunc_pntr_
private

◆ bias_cutoff_value_

double PLMD::ves::VesBias::bias_cutoff_value_
private

◆ bias_file_fmt_

std::string PLMD::ves::VesBias::bias_file_fmt_
private

◆ bias_filename_

std::string PLMD::ves::VesBias::bias_filename_
private

◆ bias_fileoutput_active_

bool PLMD::ves::VesBias::bias_fileoutput_active_
private

◆ calc_reweightfactor_

bool PLMD::ves::VesBias::calc_reweightfactor_
private

◆ coeffs_fnames

std::vector<std::string> PLMD::ves::VesBias::coeffs_fnames
private

◆ coeffs_id_prefix_

std::string PLMD::ves::VesBias::coeffs_id_prefix_
private

◆ coeffs_pntrs_

std::vector<CoeffsVector*> PLMD::ves::VesBias::coeffs_pntrs_
private

◆ comm

Communicator& PLMD::Action::comm
inherited

◆ compute_hessian_

bool PLMD::ves::VesBias::compute_hessian_
private

◆ diagonal_hessian_

bool PLMD::ves::VesBias::diagonal_hessian_
private

◆ dynamic_targetdist_

bool PLMD::ves::VesBias::dynamic_targetdist_
private

◆ dynamic_targetdist_fileoutput_active_

bool PLMD::ves::VesBias::dynamic_targetdist_fileoutput_active_
private

◆ fes_file_fmt_

std::string PLMD::ves::VesBias::fes_file_fmt_
private

◆ fes_filename_

std::string PLMD::ves::VesBias::fes_filename_
private

◆ fes_fileoutput_active_

bool PLMD::ves::VesBias::fes_fileoutput_active_
private

◆ fesproj_fileoutput_active_

bool PLMD::ves::VesBias::fesproj_fileoutput_active_
private

◆ filenames_have_iteration_number_

bool PLMD::ves::VesBias::filenames_have_iteration_number_
private

◆ files

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

◆ gradient_pntrs_

std::vector<CoeffsVector*> PLMD::ves::VesBias::gradient_pntrs_
private

◆ grid_bins_

std::vector<unsigned int> PLMD::ves::VesBias::grid_bins_
private

◆ grid_max_

std::vector<double> PLMD::ves::VesBias::grid_max_
private

◆ grid_min_

std::vector<double> PLMD::ves::VesBias::grid_min_
private

◆ hessian_pntrs_

std::vector<CoeffsMatrix*> PLMD::ves::VesBias::hessian_pntrs_
private

◆ kbt_

double PLMD::ves::VesBias::kbt_
private

◆ keywords

const Keywords& PLMD::Action::keywords
inherited

◆ log

Log& PLMD::Action::log
inherited

Reference to the log stream.

◆ multi_sim_comm

Communicator& PLMD::Action::multi_sim_comm
inherited

◆ ncoeffs_total_

size_t PLMD::ves::VesBias::ncoeffs_total_
private

◆ ncoeffssets_

unsigned int PLMD::ves::VesBias::ncoeffssets_
private

◆ optimize_coeffs_

bool PLMD::ves::VesBias::optimize_coeffs_
private

◆ optimizer_pntr_

Optimizer* PLMD::ves::VesBias::optimizer_pntr_
private

◆ plumed

PlumedMain& PLMD::Action::plumed
inherited

Reference to main plumed object.

◆ projection_args_

std::vector< std::vector<std::string> > PLMD::ves::VesBias::projection_args_
private

◆ sampled_averages

std::vector<std::vector<double> > PLMD::ves::VesBias::sampled_averages
private

◆ sampled_cross_averages

std::vector<std::vector<double> > PLMD::ves::VesBias::sampled_cross_averages
private

◆ static_targetdist_fileoutput_active_

bool PLMD::ves::VesBias::static_targetdist_fileoutput_active_
private

◆ targetdist_averages_filename_

std::string PLMD::ves::VesBias::targetdist_averages_filename_
private

◆ targetdist_averages_pntrs_

std::vector<CoeffsVector*> PLMD::ves::VesBias::targetdist_averages_pntrs_
private

◆ targetdist_file_fmt_

std::string PLMD::ves::VesBias::targetdist_file_fmt_
private

◆ targetdist_filename_

std::string PLMD::ves::VesBias::targetdist_filename_
private

◆ targetdist_pntrs_

std::vector<TargetDistribution*> PLMD::ves::VesBias::targetdist_pntrs_
private

◆ targetdist_restart_file_fmt_

std::string PLMD::ves::VesBias::targetdist_restart_file_fmt_
private

◆ use_multiple_coeffssets_

bool PLMD::ves::VesBias::use_multiple_coeffssets_
private

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