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::BasisFunctions Class Referenceabstract

#include <BasisFunctions.h>

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

typedef std::vector< Action * > Dependencies
 

Public Member Functions

 BasisFunctions (const ActionOptions &ao)
 
bool hasBeenSet () const
 
std::string getType () const
 
std::string getDescription () const
 
unsigned int getOrder () const
 
unsigned int getNumberOfBasisFunctions () const
 
unsigned int numberOfBasisFunctions () const
 
unsigned int getSize () const
 
bool arePeriodic () const
 
bool intervalBounded () const
 
double intervalMin () const
 
double intervalMax () const
 
double intervalRange () const
 
double intervalMean () const
 
double intervalDerivf () const
 
std::string intervalMinStr () const
 
std::string intervalMaxStr () const
 
std::vector< double > getUniformIntegrals () const
 
std::vector< double > getTargetDistributionIntegrals (const TargetDistribution *) const
 
std::vector< std::string > getKeywordList () const
 
std::string getKeywordString () const
 
std::string getBasisFunctionLabel (const unsigned int index) const
 
std::vector< std::string > getBasisFunctionLabels () const
 
void linkVesBias (VesBias *)
 
void linkAction (Action *)
 
VesBias * getPntrToVesBias () const
 
Action * getPntrToAction () const
 
double translateArgument (const double, bool &) const
 
double checkIfArgumentInsideInterval (const double, bool &) const
 
void apply ()
 Apply an Action. More...
 
void calculate ()
 Calculate an Action. More...
 
double getValue (const double, const unsigned int, double &, bool &) const
 
virtual void getAllValues (const double, double &, bool &, std::vector< double > &, std::vector< double > &) const =0
 
void printInfo () const
 
void getMultipleValue (const std::vector< double > &, std::vector< double > &, std::vector< std::vector< double > > &, std::vector< std::vector< double > > &, const bool numerical_deriv=false) const
 
void writeBasisFunctionsToFile (OFile &, OFile &, const std::string &min_in, const std::string &max_in, unsigned int nbins=1000, const bool ignore_periodicity=false, const std::string &output_fmt="%15.8f", const bool numerical_deriv=false) const
 
bool checkUpdate () const
 Check if action should be updated. More...
 
void addDependency (Action *)
 Specify that this Action depends on another one. More...
 
void clearDependencies ()
 Clear the dependence list for this Action. More...
 
long int getStep () const
 Return the present timestep. More...
 
double getTime () const
 Return the present time. More...
 
double getTimeStep () const
 Return the timestep. More...
 
bool getRestart () const
 Return true if we are doing a restart. More...
 
bool getCPT () const
 Return true if we are doing at a checkpoint step. More...
 
std::string getKeyword (const std::string &key)
 Just read one of the keywords and return the whole thing as a string. More...
 
template<class T >
void parse (const std::string &key, T &t)
 Parse one keyword as generic type. More...
 
template<class T >
bool parseNumbered (const std::string &key, const int no, T &t)
 Parse one numbered keyword as generic type. More...
 
template<class T >
void parseVector (const std::string &key, std::vector< T > &t)
 Parse one keyword as std::vector. More...
 
template<class T >
bool parseNumberedVector (const std::string &key, const int no, std::vector< T > &t)
 Parse a vector with a number. More...
 
void parseFlag (const std::string &key, bool &t)
 Parse one keyword as boolean flag. More...
 
void error (const std::string &msg) const
 Crash calculation and print documentation. More...
 
void warning (const std::string &msg)
 Issue a warning. More...
 
void exit (int c=0)
 Exit with error code c. More...
 
void checkRead ()
 Check if Action was properly read. More...
 
virtual void prepare ()
 Prepare an Action for calculation This can be used by Action if they need some special preparation before calculation. More...
 
virtual void lockRequests ()
 
virtual void unlockRequests ()
 
virtual void beforeUpdate ()
 Before Update. More...
 
virtual void update ()
 Update. More...
 
virtual void runFinalJobs ()
 RunFinalJobs This method is called once at the very end of the calculation. More...
 
void fflush ()
 Tell to the Action to flush open files. More...
 
virtual std::string getDocumentation () const
 
const std::string & getLabel () const
 Returns the label. More...
 
const std::string & getName () const
 Returns the name. More...
 
virtual void activate ()
 Set action to active. More...
 
virtual void setOption (const std::string &s)
 
virtual void clearOptions ()
 
virtual void deactivate ()
 Set action to inactive. More...
 
bool isActive () const
 Check if action is active. More...
 
bool isOptionOn (const std::string &s) const
 Check if an option is on. More...
 
const Dependencies & getDependencies () const
 Return dependencies. More...
 
virtual bool checkNumericalDerivatives () const
 Check if numerical derivatives should be performed. More...
 
virtual bool checkNeedsGradients () const
 Check if the action needs gradient. More...
 
virtual void calculateNumericalDerivatives (ActionWithValue *a=NULL)
 Perform calculation using numerical derivatives N.B. More...
 
FILE * fopen (const char *path, const char *mode)
 Opens a file. More...
 
int fclose (FILE *fp)
 Closes a file opened with Action::fclose(). More...
 
void calculateFromPDB (const PDB &)
 Calculate the action given a pdb file as input. More...
 
virtual void readAtomsFromPDB (const PDB &)
 This is overwritten in ActionAtomistic so that we can read the atoms from the pdb input file rather than taking them from the MD code. More...
 
bool getExchangeStep () const
 Check if we are on an exchange step. More...
 
std::string cite (const std::string &s)
 Cite a paper see PlumedMain::cite. More...
 

Static Public Member Functions

static void registerKeywords (Keywords &)
 

Public Attributes

PlumedMain & plumed
 Reference to main plumed object. More...
 
Log & log
 Reference to the log stream. More...
 
std::set< FILE * > files
 
Communicator & comm
 
Communicator & multi_sim_comm
 
const Keywords & keywords
 

Protected Member Functions

void setupBF ()
 
void setupInterval ()
 
void setNumericalIntegrationBins (const unsigned int nbins)
 
void numericalUniformIntegrals ()
 
std::vector< double > numericalTargetDistributionIntegralsFromGrid (const Grid *) const
 
virtual void setupLabels ()
 
virtual void setupUniformIntegrals ()
 
template<typename T >
void addKeywordToList (const std::string &, const T)
 
template<typename T >
void addKeywordToList (const std::string &, const std::vector< T > &)
 
void addKeywordToList (const std::string &, const bool)
 
void setPeriodic ()
 
void setNonPeriodic ()
 
void setIntervalBounded ()
 
void setIntervalNonBounded ()
 
void setType (const std::string &type_in)
 
void setDescription (const std::string &description_in)
 
void setNumberOfBasisFunctions (const unsigned int)
 
void setOrder (const unsigned int norder_in)
 
void setIntrinsicInterval (const double, const double)
 
void setIntrinsicInterval (const std::string &, const std::string &)
 
void setInterval (const double, const double)
 
void setInterval (const std::string &, const std::string &)
 
double intrinsicIntervalMin () const
 
double intrinsicIntervalMax () const
 
std::string intrinsicIntervalMinStr () const
 
std::string intrinsicIntervalMaxStr () const
 
void setUniformIntegral (const unsigned int, const double)
 
void setUniformIntegrals (const std::vector< double > &)
 
void setAllUniformIntegralsToZero ()
 
void setLabelPrefix (const std::string &)
 
void setLabel (const unsigned int, const std::string &)
 
void setLabels (const std::vector< std::string > &)
 

Private Member Functions

void getAllValuesNumericalDerivs (const double, double &, bool &, std::vector< double > &, std::vector< double > &) const
 

Private Attributes

bool print_debug_info_
 
bool has_been_set
 
std::string description_
 
std::string type_
 
unsigned int norder_
 
unsigned int nbasis_
 
std::vector< std::string > bf_keywords_
 
std::string bf_label_prefix_
 
std::vector< std::string > bf_labels_
 
bool periodic_
 
bool interval_bounded_
 
std::string interval_intrinsic_min_str_
 
std::string interval_intrinsic_max_str_
 
double interval_intrinsic_min_
 
double interval_intrinsic_max_
 
double interval_intrinsic_range_
 
double interval_intrinsic_mean_
 
std::string interval_min_str_
 
std::string interval_max_str_
 
double interval_min_
 
double interval_max_
 
double interval_range_
 
double interval_mean_
 
double argT_derivf_
 
bool numerical_uniform_integrals_
 
unsigned int nbins_
 
std::vector< double > uniform_integrals_
 
VesBias * vesbias_pntr_
 
Action * action_pntr_
 

Member Typedef Documentation

◆ Dependencies

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

Constructor & Destructor Documentation

◆ BasisFunctions()

PLMD::ves::BasisFunctions::BasisFunctions ( const ActionOptions &  ao)
explicit

Member Function Documentation

◆ activate()

void PLMD::Action::activate ( )
virtualinherited

Set action to active.

◆ addDependency()

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

Specify that this Action depends on another one.

◆ addKeywordToList() [1/3]

template<typename T >
void PLMD::ves::BasisFunctions::addKeywordToList ( const std::string &  keyword,
const T  value 
)
protected

◆ addKeywordToList() [2/3]

template<typename T >
void PLMD::ves::BasisFunctions::addKeywordToList ( const std::string &  keyword,
const std::vector< T > &  values 
)
protected

◆ addKeywordToList() [3/3]

void PLMD::ves::BasisFunctions::addKeywordToList ( const std::string &  keyword,
const bool  value 
)
inlineprotected

◆ apply()

void PLMD::ves::BasisFunctions::apply ( )
inlinevirtual

Apply an Action.

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

Implements PLMD::Action.

◆ arePeriodic()

bool PLMD::ves::BasisFunctions::arePeriodic ( ) 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.

◆ calculate()

void PLMD::ves::BasisFunctions::calculate ( )
inlinevirtual

Calculate an Action.

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

Implements PLMD::Action.

◆ 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::Action::calculateNumericalDerivatives ( ActionWithValue *  a = NULL)
virtualinherited

Perform calculation using numerical derivatives N.B.

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

Reimplemented in PLMD::isdb::MetainferenceBase, PLMD::mapping::PCAVars, PLMD::multicolvar::MultiColvarBase, PLMD::ActionAtomistic, PLMD::multicolvar::DumpMultiColvar, PLMD::ActionWithArguments, PLMD::multicolvar::BridgedMultiColvarFunction, PLMD::vesselbase::ActionWithAveraging, PLMD::mapping::Mapping, and PLMD::vesselbase::ActionWithInputVessel.

◆ checkIfArgumentInsideInterval()

double PLMD::ves::BasisFunctions::checkIfArgumentInsideInterval ( const double  arg,
bool &  inside_interval 
) const
inline

◆ 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()

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

Check if numerical derivatives should be performed.

Reimplemented in PLMD::ActionWithValue.

◆ checkRead()

void PLMD::Action::checkRead ( )
inherited

Check if Action was properly read.

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

◆ checkUpdate()

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

Check if action should be updated.

◆ cite()

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

Cite a paper see PlumedMain::cite.

◆ clearDependencies()

void PLMD::Action::clearDependencies ( )
inherited

Clear the dependence list for this Action.

◆ clearOptions()

void PLMD::Action::clearOptions ( )
virtualinherited

◆ deactivate()

void PLMD::Action::deactivate ( )
inlinevirtualinherited

Set action to inactive.

◆ error()

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

Crash calculation and print documentation.

◆ exit()

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

Exit with error code c.

◆ 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)

◆ getAllValues()

virtual void PLMD::ves::BasisFunctions::getAllValues ( const double  ,
double &  ,
bool &  ,
std::vector< double > &  ,
std::vector< double > &   
) const
pure virtual

Implemented in PLMD::ves::BF_Custom, PLMD::ves::BF_Legendre, PLMD::ves::BF_Chebyshev, PLMD::ves::BF_Fourier, PLMD::ves::BF_Cosine, PLMD::ves::BF_Sine, PLMD::ves::BF_Powers, and PLMD::ves::BF_Combined.

◆ getAllValuesNumericalDerivs()

void PLMD::ves::BasisFunctions::getAllValuesNumericalDerivs ( const double  arg,
double &  argT,
bool &  inside_range,
std::vector< double > &  values,
std::vector< double > &  derivs 
) const
private

◆ getBasisFunctionLabel()

std::string PLMD::ves::BasisFunctions::getBasisFunctionLabel ( const unsigned int  index) const
inline

◆ getBasisFunctionLabels()

std::vector<std::string> PLMD::ves::BasisFunctions::getBasisFunctionLabels ( ) const
inline

◆ 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.

◆ getDescription()

std::string PLMD::ves::BasisFunctions::getDescription ( ) const
inline

◆ getDocumentation()

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

◆ getExchangeStep()

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

Check if we are on an exchange step.

◆ 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.

◆ getKeywordList()

std::vector<std::string> PLMD::ves::BasisFunctions::getKeywordList ( ) const
inline

◆ getKeywordString()

std::string PLMD::ves::BasisFunctions::getKeywordString ( ) const

◆ getLabel()

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

Returns the label.

◆ getMultipleValue()

void PLMD::ves::BasisFunctions::getMultipleValue ( const std::vector< double > &  args,
std::vector< double > &  argsT,
std::vector< std::vector< double > > &  values,
std::vector< std::vector< double > > &  derivs,
const bool  numerical_deriv = false 
) const

◆ getName()

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

Returns the name.

◆ getNumberOfBasisFunctions()

unsigned int PLMD::ves::BasisFunctions::getNumberOfBasisFunctions ( ) const
inline

◆ getOrder()

unsigned int PLMD::ves::BasisFunctions::getOrder ( ) const
inline

◆ getPntrToAction()

Action * PLMD::ves::BasisFunctions::getPntrToAction ( ) const
inline

◆ getPntrToVesBias()

VesBias * PLMD::ves::BasisFunctions::getPntrToVesBias ( ) const
inline

◆ getRestart()

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

Return true if we are doing a restart.

◆ getSize()

unsigned int PLMD::ves::BasisFunctions::getSize ( ) const
inline

◆ getStep()

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

Return the present timestep.

◆ getTargetDistributionIntegrals()

std::vector< double > PLMD::ves::BasisFunctions::getTargetDistributionIntegrals ( const TargetDistribution *  targetdist_pntr) const

◆ getTime()

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

Return the present time.

◆ getTimeStep()

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

Return the timestep.

◆ getType()

std::string PLMD::ves::BasisFunctions::getType ( ) const
inline

◆ getUniformIntegrals()

std::vector<double> PLMD::ves::BasisFunctions::getUniformIntegrals ( ) const
inline

◆ getValue()

double PLMD::ves::BasisFunctions::getValue ( const double  arg,
const unsigned int  n,
double &  argT,
bool &  inside_range 
) const

◆ hasBeenSet()

bool PLMD::ves::BasisFunctions::hasBeenSet ( ) const
inline

◆ intervalBounded()

bool PLMD::ves::BasisFunctions::intervalBounded ( ) const
inline

◆ intervalDerivf()

double PLMD::ves::BasisFunctions::intervalDerivf ( ) const
inline

◆ intervalMax()

double PLMD::ves::BasisFunctions::intervalMax ( ) const
inline

◆ intervalMaxStr()

std::string PLMD::ves::BasisFunctions::intervalMaxStr ( ) const
inline

◆ intervalMean()

double PLMD::ves::BasisFunctions::intervalMean ( ) const
inline

◆ intervalMin()

double PLMD::ves::BasisFunctions::intervalMin ( ) const
inline

◆ intervalMinStr()

std::string PLMD::ves::BasisFunctions::intervalMinStr ( ) const
inline

◆ intervalRange()

double PLMD::ves::BasisFunctions::intervalRange ( ) const
inline

◆ intrinsicIntervalMax()

double PLMD::ves::BasisFunctions::intrinsicIntervalMax ( ) const
inlineprotected

◆ intrinsicIntervalMaxStr()

std::string PLMD::ves::BasisFunctions::intrinsicIntervalMaxStr ( ) const
inlineprotected

◆ intrinsicIntervalMin()

double PLMD::ves::BasisFunctions::intrinsicIntervalMin ( ) const
inlineprotected

◆ intrinsicIntervalMinStr()

std::string PLMD::ves::BasisFunctions::intrinsicIntervalMinStr ( ) const
inlineprotected

◆ 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.

◆ linkAction()

void PLMD::ves::BasisFunctions::linkAction ( Action *  action_pntr_in)

◆ linkVesBias()

void PLMD::ves::BasisFunctions::linkVesBias ( VesBias *  vesbias_pntr_in)

◆ lockRequests()

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

Reimplemented in PLMD::isdb::MetainferenceBase, PLMD::mapping::PCAVars, PLMD::ActionAtomistic, PLMD::ActionWithArguments, PLMD::mapping::Mapping, and PLMD::vesselbase::ActionWithAveraging.

◆ numberOfBasisFunctions()

unsigned int PLMD::ves::BasisFunctions::numberOfBasisFunctions ( ) const
inline

◆ numericalTargetDistributionIntegralsFromGrid()

std::vector< double > PLMD::ves::BasisFunctions::numericalTargetDistributionIntegralsFromGrid ( const Grid *  grid_pntr) const
protected

◆ numericalUniformIntegrals()

void PLMD::ves::BasisFunctions::numericalUniformIntegrals ( )
protected

◆ parse()

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

Parse one keyword as generic type.

◆ 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.

◆ prepare()

void PLMD::Action::prepare ( )
virtualinherited

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

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

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

◆ printInfo()

void PLMD::ves::BasisFunctions::printInfo ( ) const

◆ 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.

◆ registerKeywords()

void PLMD::ves::BasisFunctions::registerKeywords ( Keywords &  keys)
static

◆ 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::analysis::Analysis, PLMD::gridtools::ConvertToFES, and PLMD::gridtools::GridPrintingBase.

◆ setAllUniformIntegralsToZero()

void PLMD::ves::BasisFunctions::setAllUniformIntegralsToZero ( )
inlineprotected

◆ setDescription()

void PLMD::ves::BasisFunctions::setDescription ( const std::string &  description_in)
inlineprotected

◆ setInterval() [1/2]

void PLMD::ves::BasisFunctions::setInterval ( const double  interval_min_in,
const double  interval_max_in 
)
protected

◆ setInterval() [2/2]

void PLMD::ves::BasisFunctions::setInterval ( const std::string &  interval_min_str_in,
const std::string &  interval_max_str_in 
)
protected

◆ setIntervalBounded()

void PLMD::ves::BasisFunctions::setIntervalBounded ( )
inlineprotected

◆ setIntervalNonBounded()

void PLMD::ves::BasisFunctions::setIntervalNonBounded ( )
inlineprotected

◆ setIntrinsicInterval() [1/2]

void PLMD::ves::BasisFunctions::setIntrinsicInterval ( const double  interval_intrinsic_min_in,
const double  interval_intrinsic_max_in 
)
protected

◆ setIntrinsicInterval() [2/2]

void PLMD::ves::BasisFunctions::setIntrinsicInterval ( const std::string &  interval_intrinsic_min_str_in,
const std::string &  interval_intrinsic_max_str_in 
)
protected

◆ setLabel()

void PLMD::ves::BasisFunctions::setLabel ( const unsigned int  index,
const std::string &  label 
)
inlineprotected

◆ setLabelPrefix()

void PLMD::ves::BasisFunctions::setLabelPrefix ( const std::string &  bf_label_prefix_in)
inlineprotected

◆ setLabels()

void PLMD::ves::BasisFunctions::setLabels ( const std::vector< std::string > &  bf_labels_in)
inlineprotected

◆ setNonPeriodic()

void PLMD::ves::BasisFunctions::setNonPeriodic ( )
inlineprotected

◆ setNumberOfBasisFunctions()

void PLMD::ves::BasisFunctions::setNumberOfBasisFunctions ( const unsigned int  nbasis_in)
inlineprotected

◆ setNumericalIntegrationBins()

void PLMD::ves::BasisFunctions::setNumericalIntegrationBins ( const unsigned int  nbins)
inlineprotected

◆ setOption()

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

◆ setOrder()

void PLMD::ves::BasisFunctions::setOrder ( const unsigned int  norder_in)
inlineprotected

◆ setPeriodic()

void PLMD::ves::BasisFunctions::setPeriodic ( )
inlineprotected

◆ setType()

void PLMD::ves::BasisFunctions::setType ( const std::string &  type_in)
inlineprotected

◆ setUniformIntegral()

void PLMD::ves::BasisFunctions::setUniformIntegral ( const unsigned  int,
const double  value 
)
inlineprotected

◆ setUniformIntegrals()

void PLMD::ves::BasisFunctions::setUniformIntegrals ( const std::vector< double > &  uniform_integrals_in)
inlineprotected

◆ setupBF()

void PLMD::ves::BasisFunctions::setupBF ( )
protected

◆ setupInterval()

void PLMD::ves::BasisFunctions::setupInterval ( )
protected

◆ setupLabels()

void PLMD::ves::BasisFunctions::setupLabels ( )
protectedvirtual

Reimplemented in PLMD::ves::BF_Fourier, PLMD::ves::BF_Cosine, PLMD::ves::BF_Sine, PLMD::ves::BF_Powers, and PLMD::ves::BF_Combined.

◆ setupUniformIntegrals()

void PLMD::ves::BasisFunctions::setupUniformIntegrals ( )
protectedvirtual

Reimplemented in PLMD::ves::BF_Legendre, PLMD::ves::BF_Chebyshev, PLMD::ves::BF_Fourier, PLMD::ves::BF_Cosine, PLMD::ves::BF_Sine, and PLMD::ves::BF_Combined.

◆ translateArgument()

double PLMD::ves::BasisFunctions::translateArgument ( const double  arg,
bool &  inside_interval 
) const
inline

◆ unlockRequests()

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

Reimplemented in PLMD::isdb::MetainferenceBase, PLMD::mapping::PCAVars, PLMD::ActionAtomistic, PLMD::ActionWithArguments, PLMD::mapping::Mapping, and PLMD::vesselbase::ActionWithAveraging.

◆ update()

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

Update.

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

Reimplemented in PLMD::isdb::CS2Backbone, PLMD::bias::MetaD, PLMD::bias::PBMetaD, PLMD::isdb::Metainference, PLMD::ves::Optimizer, PLMD::isdb::RDC, PLMD::eds::EDS, PLMD::ves::TargetDistribution, PLMD::bias::MaxEnt, PLMD::generic::DumpAtoms, PLMD::multicolvar::VolumeTetrapore, PLMD::bias::ExtendedLagrangian, PLMD::multicolvar::VolumeCavity, PLMD::generic::EffectiveEnergyDrift, PLMD::isdb::SAXS, PLMD::generic::DumpMassCharge, PLMD::isdb::JCoupling, PLMD::mapping::AdaptivePath, PLMD::generic::Print, PLMD::ves::OutputFesBias, PLMD::isdb::PRE, PLMD::adjmat::OutputCluster, PLMD::generic::Read, PLMD::isdb::NOE, PLMD::multicolvar::DumpMultiColvar, PLMD::vesselbase::ActionWithAveraging, PLMD::generic::Flush, PLMD::generic::DumpDerivatives, PLMD::generic::DumpForces, PLMD::generic::DumpProjections, PLMD::adjmat::DumpGraph, and PLMD::gridtools::GridPrintingBase.

◆ warning()

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

Issue a warning.

◆ writeBasisFunctionsToFile()

void PLMD::ves::BasisFunctions::writeBasisFunctionsToFile ( OFile &  ofile_values,
OFile &  ofile_derivs,
const std::string &  min_in,
const std::string &  max_in,
unsigned int  nbins = 1000,
const bool  ignore_periodicity = false,
const std::string &  output_fmt = "%15.8f",
const bool  numerical_deriv = false 
) const

Member Data Documentation

◆ action_pntr_

Action* PLMD::ves::BasisFunctions::action_pntr_
private

◆ argT_derivf_

double PLMD::ves::BasisFunctions::argT_derivf_
private

◆ bf_keywords_

std::vector<std::string> PLMD::ves::BasisFunctions::bf_keywords_
private

◆ bf_label_prefix_

std::string PLMD::ves::BasisFunctions::bf_label_prefix_
private

◆ bf_labels_

std::vector<std::string> PLMD::ves::BasisFunctions::bf_labels_
private

◆ comm

Communicator& PLMD::Action::comm
inherited

◆ description_

std::string PLMD::ves::BasisFunctions::description_
private

◆ files

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

◆ has_been_set

bool PLMD::ves::BasisFunctions::has_been_set
private

◆ interval_bounded_

bool PLMD::ves::BasisFunctions::interval_bounded_
private

◆ interval_intrinsic_max_

double PLMD::ves::BasisFunctions::interval_intrinsic_max_
private

◆ interval_intrinsic_max_str_

std::string PLMD::ves::BasisFunctions::interval_intrinsic_max_str_
private

◆ interval_intrinsic_mean_

double PLMD::ves::BasisFunctions::interval_intrinsic_mean_
private

◆ interval_intrinsic_min_

double PLMD::ves::BasisFunctions::interval_intrinsic_min_
private

◆ interval_intrinsic_min_str_

std::string PLMD::ves::BasisFunctions::interval_intrinsic_min_str_
private

◆ interval_intrinsic_range_

double PLMD::ves::BasisFunctions::interval_intrinsic_range_
private

◆ interval_max_

double PLMD::ves::BasisFunctions::interval_max_
private

◆ interval_max_str_

std::string PLMD::ves::BasisFunctions::interval_max_str_
private

◆ interval_mean_

double PLMD::ves::BasisFunctions::interval_mean_
private

◆ interval_min_

double PLMD::ves::BasisFunctions::interval_min_
private

◆ interval_min_str_

std::string PLMD::ves::BasisFunctions::interval_min_str_
private

◆ interval_range_

double PLMD::ves::BasisFunctions::interval_range_
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

◆ nbasis_

unsigned int PLMD::ves::BasisFunctions::nbasis_
private

◆ nbins_

unsigned int PLMD::ves::BasisFunctions::nbins_
private

◆ norder_

unsigned int PLMD::ves::BasisFunctions::norder_
private

◆ numerical_uniform_integrals_

bool PLMD::ves::BasisFunctions::numerical_uniform_integrals_
private

◆ periodic_

bool PLMD::ves::BasisFunctions::periodic_
private

◆ plumed

PlumedMain& PLMD::Action::plumed
inherited

Reference to main plumed object.

◆ print_debug_info_

bool PLMD::ves::BasisFunctions::print_debug_info_
private

◆ type_

std::string PLMD::ves::BasisFunctions::type_
private

◆ uniform_integrals_

std::vector<double> PLMD::ves::BasisFunctions::uniform_integrals_
private

◆ vesbias_pntr_

VesBias* PLMD::ves::BasisFunctions::vesbias_pntr_
private
The documentation for this class was generated from the following files:
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