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
[legend]

Public Types

typedef std::vector< Action * > Dependencies
 

Public Member Functions

 BasisFunctions (const ActionOptions &ao)
 
virtual void activate ()
 Set action to active. More...
 
void addDependency (Action *)
 Specify that this Action depends on another one. More...
 
void apply () override
 Apply an Action. More...
 
bool arePeriodic () const
 
virtual void beforeUpdate ()
 Before Update. More...
 
void calculate () override
 Calculate an Action. More...
 
void calculateFromPDB (const PDB &)
 Calculate the action given a pdb file as input. More...
 
virtual void calculateNumericalDerivatives (ActionWithValue *a=NULL)
 Perform calculation using numerical derivatives N.B. More...
 
virtual ActionAtomistic * castToActionAtomistic () noexcept
 
virtual ActionForInterface * castToActionForInterface () noexcept
 
virtual ActionShortcut * castToActionShortcut () noexcept
 
virtual ActionToGetData * castToActionToGetData () noexcept
 
virtual ActionToPutData * castToActionToPutData () noexcept
 
virtual ActionWithArguments * castToActionWithArguments () noexcept
 
virtual ActionWithValue * castToActionWithValue () noexcept
 Specialized casts, to make PlumedMain run faster. More...
 
virtual ActionWithVirtualAtom * castToActionWithVirtualAtom () noexcept
 
virtual DomainDecomposition * castToDomainDecomposition () noexcept
 
virtual PbcAction * castToPbcAction () noexcept
 
bool checkForDependency (Action *)
 Check that this action does not depend on the action in the argument. More...
 
double checkIfArgumentInsideInterval (const double, bool &) const
 
virtual bool checkNeedsGradients () const
 Check if the action needs gradient. 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 clearOptions ()
 
virtual void deactivate ()
 Set action to inactive. More...
 
void error (const std::string &msg) const
 Crash calculation and print documentation. 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...
 
virtual void getAllValues (const double, double &, bool &, std::vector< double > &, std::vector< double > &) const =0
 
std::string getBasisFunctionLabel (const unsigned int index) const
 
std::vector< std::string > getBasisFunctionLabels () const
 
bool getCPT () const
 Return true if we are doing at a checkpoint step. More...
 
std::string getDefaultString () const
 Get the defaults. More...
 
const Dependencies & getDependencies () const
 Return dependencies. More...
 
std::string getDescription () const
 
bool getExchangeStep () const
 Check if we are on an exchange step. More...
 
double getkBT ()
 Get the value of kBT by either reading the TEMP keyword and multiplying the temperature by Boltzmann's constant or get it fro the MD code. More...
 
std::string getKeyword (const std::string &key)
 Just read one of the keywords and return the whole thing as a string. More...
 
std::vector< std::string > getKeywordList () const
 
std::string getKeywordString () const
 
const std::string & getLabel () const
 Returns the label. More...
 
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
 
const std::string & getName () const
 Returns the name. More...
 
unsigned int getNumberOfBasisFunctions () const
 
unsigned int getOrder () const
 
Action * getPntrToAction () const
 
VesBias * getPntrToVesBias () const
 
bool getRestart () const
 Return true if we are doing a restart. More...
 
unsigned int getSize () const
 
long long int getStep () const
 Return the present timestep. More...
 
std::vector< double > getTargetDistributionIntegrals (const TargetDistribution *) const
 
double getTime () const
 Return the present time. More...
 
double getTimeStep () const
 Return the timestep. More...
 
std::string getType () const
 
std::vector< double > getUniformIntegrals () const
 
double getValue (const double, const unsigned int, double &, bool &) const
 
bool hasBeenSet () const
 
bool intervalBounded () const
 
double intervalDerivf () const
 
double intervalMax () const
 
std::string intervalMaxStr () const
 
double intervalMean () const
 
double intervalMin () const
 
std::string intervalMinStr () const
 
double intervalRange () const
 
bool isActive () const
 Check if action is active. More...
 
bool isOptionOn (const std::string &s) const
 Check if an option is on. More...
 
void linkAction (Action *)
 
void linkVesBias (VesBias *)
 
virtual void lockRequests ()
 
unsigned int numberOfBasisFunctions () const
 
template<class T >
void parse (const std::string &key, T &t)
 Parse one keyword as generic type. 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...
 
void printInfo () const
 
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 resetStoredTimestep ()
 Set the timestep that is stored in the action to the correct value. More...
 
virtual void runFinalJobs ()
 RunFinalJobs This method is called once at the very end of the calculation. More...
 
virtual void setOption (const std::string &s)
 
void setupConstantValues (const bool &have_atoms)
 This calculates any values that are constant and ensures that we don't calculate these actions on every timestep. More...
 
double translateArgument (const double, bool &) const
 
virtual void unlockRequests ()
 
virtual void update ()
 Update. More...
 
void warning (const std::string &msg)
 Issue a warning. More...
 
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_values="%15.8f", const std::string &output_fmt_derivs="%15.8f", const bool numerical_deriv=false) const
 
virtual std::string writeInGraph () const
 Get the info on what to calculate. More...
 

Static Public Member Functions

static void registerKeywords (Keywords &)
 

Public Attributes

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

Protected Member Functions

void addKeywordToList (const std::string &, const bool)
 
template<typename T >
void addKeywordToList (const std::string &, const std::vector< T > &)
 
template<typename T >
void addKeywordToList (const std::string &, const T)
 
double getKBoltzmann () const
 Get the value of Boltzmann's constant. More...
 
const Units & getUnits () const
 Get the units that we are operating in. More...
 
double intrinsicIntervalMax () const
 
std::string intrinsicIntervalMaxStr () const
 
double intrinsicIntervalMin () const
 
std::string intrinsicIntervalMinStr () const
 
std::vector< double > numericalTargetDistributionIntegralsFromGrid (const Grid *) const
 
void numericalUniformIntegrals ()
 
void setAllUniformIntegralsToZero ()
 
void setDescription (const std::string &description_in)
 
void setInterval (const double, const double)
 
void setInterval (const std::string &, const std::string &)
 
void setIntervalBounded ()
 
void setIntervalNonBounded ()
 
void setIntrinsicInterval (const double, const double)
 
void setIntrinsicInterval (const std::string &, const std::string &)
 
void setLabel (const unsigned int, const std::string &)
 
void setLabelPrefix (const std::string &)
 
void setLabels (const std::vector< std::string > &)
 
void setNonPeriodic ()
 
void setNumberOfBasisFunctions (const unsigned int)
 
void setNumericalIntegrationBins (const unsigned int nbins)
 
void setOrder (const unsigned int norder_in)
 
void setPeriodic ()
 
void setType (const std::string &type_in)
 
void setUniformIntegral (const unsigned int, const double)
 
void setUniformIntegrals (const std::vector< double > &)
 
void setupBF ()
 
void setupInterval ()
 
virtual void setupLabels ()
 
virtual void setupUniformIntegrals ()
 
bool usingNaturalUnits () const
 Are we using natural units. More...
 

Private Member Functions

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

Private Attributes

Action * action_pntr_
 
bool active
 Switch to activate Action on this step. More...
 
Dependencies after
 Actions on which this Action depends. More...
 
double argT_derivf_
 
std::vector< std::string > bf_keywords_
 
std::string bf_label_prefix_
 
std::vector< std::string > bf_labels_
 
std::string defaults
 The set of default arguments that we are using. More...
 
std::string description_
 
bool doCheckPoint
 
bool has_been_set
 
bool interval_bounded_
 
double interval_intrinsic_max_
 
std::string interval_intrinsic_max_str_
 
double interval_intrinsic_mean_
 
double interval_intrinsic_min_
 
std::string interval_intrinsic_min_str_
 
double interval_intrinsic_range_
 
double interval_max_
 
std::string interval_max_str_
 
double interval_mean_
 
double interval_min_
 
std::string interval_min_str_
 
double interval_range_
 
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...
 
const std::string name
 Name of the directive in the plumed.dat file. More...
 
unsigned int nbasis_
 
unsigned int nbins_
 
bool never_activate
 
unsigned int norder_
 
bool numerical_uniform_integrals_
 
std::set< std::string > options
 Option that you might have enabled. More...
 
bool periodic_
 
bool print_debug_info_
 
int replica_index
 
bool restart
 
double timestep
 Save the timestep here. More...
 
std::string type_
 
std::vector< double > uniform_integrals_
 
double update_from
 Update only after this time. More...
 
double update_until
 Update only until this time. More...
 
VesBias * vesbias_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]

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

◆ addKeywordToList() [2/3]

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

◆ addKeywordToList() [3/3]

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

◆ apply()

void PLMD::ves::BasisFunctions::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.

◆ 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 ( )
inlineoverridevirtual

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::ActionWithVector, PLMD::ActionAtomistic, PLMD::generic::DumpAtoms, PLMD::ActionWithArguments, PLMD::generic::PrintNDX, PLMD::isdb::EMMI, PLMD::isdb::MetainferenceBase, and PLMD::contour::DistanceFromContourBase.

◆ castToActionAtomistic()

virtual ActionAtomistic* PLMD::Action::castToActionAtomistic ( )
inlinevirtualnoexceptinherited

Reimplemented in PLMD::ActionAtomistic.

◆ castToActionForInterface()

virtual ActionForInterface* PLMD::Action::castToActionForInterface ( )
inlinevirtualnoexceptinherited

Reimplemented in PLMD::ActionForInterface.

◆ castToActionShortcut()

virtual ActionShortcut* PLMD::Action::castToActionShortcut ( )
inlinevirtualnoexceptinherited

Reimplemented in PLMD::ActionShortcut.

◆ castToActionToGetData()

virtual ActionToGetData* PLMD::Action::castToActionToGetData ( )
inlinevirtualnoexceptinherited

Reimplemented in PLMD::ActionToGetData.

◆ castToActionToPutData()

virtual ActionToPutData* PLMD::Action::castToActionToPutData ( )
inlinevirtualnoexceptinherited

Reimplemented in PLMD::ActionToPutData.

◆ castToActionWithArguments()

virtual ActionWithArguments* PLMD::Action::castToActionWithArguments ( )
inlinevirtualnoexceptinherited

Reimplemented in PLMD::ActionWithArguments.

◆ castToActionWithValue()

virtual ActionWithValue* PLMD::Action::castToActionWithValue ( )
inlinevirtualnoexceptinherited

Specialized casts, to make PlumedMain run faster.

Reimplemented in PLMD::ActionWithValue.

◆ castToActionWithVirtualAtom()

virtual ActionWithVirtualAtom* PLMD::Action::castToActionWithVirtualAtom ( )
inlinevirtualnoexceptinherited

Reimplemented in PLMD::ActionWithVirtualAtom.

◆ castToDomainDecomposition()

virtual DomainDecomposition* PLMD::Action::castToDomainDecomposition ( )
inlinevirtualnoexceptinherited

Reimplemented in PLMD::DomainDecomposition.

◆ castToPbcAction()

virtual PbcAction* PLMD::Action::castToPbcAction ( )
inlinevirtualnoexceptinherited

Reimplemented in PLMD::PbcAction.

◆ checkForDependency()

bool PLMD::Action::checkForDependency ( Action *  action)
inherited

Check that this action does not depend on the action in the argument.

◆ 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_Wavelets, PLMD::ves::BF_Custom, PLMD::ves::BF_Gaussians, PLMD::ves::BF_Legendre, PLMD::ves::BF_Chebyshev, PLMD::ves::BF_Fourier, PLMD::ves::BF_Cosine, PLMD::ves::BF_Sine, PLMD::ves::BF_Powers, PLMD::ves::BF_Combined, and PLMD::ves::BF_CubicBsplines.

◆ 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.

◆ getDefaultString()

std::string PLMD::Action::getDefaultString ( ) const
inlineinherited

Get the defaults.

◆ getDependencies()

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

Return dependencies.

◆ getDescription()

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

◆ getExchangeStep()

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

Check if we are on an exchange step.

◆ getKBoltzmann()

double PLMD::Action::getKBoltzmann ( ) const
protectedinherited

Get the value of Boltzmann's constant.

◆ getkBT()

double PLMD::Action::getkBT ( )
inherited

Get the value of kBT by either reading the TEMP keyword and multiplying the temperature by Boltzmann's constant or get it fro the MD code.

◆ 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 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

◆ getUnits()

const Units & PLMD::Action::getUnits ( ) const
protectedinherited

Get the units that we are operating in.

◆ 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::EMMI, PLMD::isdb::MetainferenceBase, PLMD::ActionAtomistic, PLMD::generic::DumpAtoms, PLMD::ActionWithVector, PLMD::ActionWithArguments, PLMD::generic::PrintNDX, and PLMD::contour::DistanceFromContourBase.

◆ 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::function::FuncPathMSD, PLMD::generic::Plumed, PLMD::ActionWithVector, PLMD::generic::Read, PLMD::generic::DumpMassCharge, PLMD::generic::UpdateIf, PLMD::generic::Print, PLMD::GenericMolInfo, PLMD::dimred::ArrangePoints, PLMD::function::FunctionOfVector< T >, PLMD::function::FunctionOfMatrix< T >, PLMD::adjmat::AdjacencyMatrixBase, PLMD::matrixtools::MatrixTimesMatrix, PLMD::valtools::SelectWithMask, PLMD::dimred::ProjectPoints, PLMD::generic::CreateMask, PLMD::matrixtools::DiagonalizeMatrix, PLMD::matrixtools::MatrixTimesVector, PLMD::matrixtools::OuterProduct, PLMD::valtools::VStack, PLMD::landmarks::FarthestPointSampling, PLMD::colvar::CoordinationBase, PLMD::matrixtools::TransposeMatrix, PLMD::matrixtools::Voronoi, PLMD::function::FuncPathGeneral, PLMD::maze::Optimizer, and PLMD::s2cm::S2ContactModel.

◆ 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

◆ resetStoredTimestep()

void PLMD::Action::resetStoredTimestep ( )
inherited

Set the timestep that is stored in the action to the correct value.

◆ 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.

◆ 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   
)
inlineprotected

◆ setUniformIntegrals()

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

◆ setupBF()

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

◆ setupConstantValues()

void PLMD::Action::setupConstantValues ( const bool &  have_atoms)
inherited

This calculates any values that are constant and ensures that we don't calculate these actions on every timestep.

◆ setupInterval()

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

◆ setupLabels()

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

Reimplemented in PLMD::ves::BF_Wavelets, PLMD::ves::BF_Gaussians, 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::EMMI, PLMD::isdb::MetainferenceBase, PLMD::ActionAtomistic, PLMD::generic::DumpAtoms, PLMD::ActionWithVector, PLMD::ActionWithArguments, PLMD::generic::PrintNDX, and PLMD::contour::DistanceFromContourBase.

◆ 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::bias::MetaD, PLMD::isdb::CS2Backbone, PLMD::isdb::SAXS, PLMD::bias::PBMetaD, PLMD::ves::VesLinearExpansion, PLMD::isdb::Metainference, PLMD::opes::OPESmetad< mode >, PLMD::isdb::RDC, PLMD::ves::Optimizer, PLMD::gridtools::DumpGrid, PLMD::ves::TargetDistribution, PLMD::opes::OPESexpanded, PLMD::ves::VesDeltaF, PLMD::generic::Plumed, PLMD::bias::MaxEnt, PLMD::generic::DumpAtoms, PLMD::volumes::VolumeTetrapore, PLMD::volumes::VolumeCavity, PLMD::generic::EffectiveEnergyDrift, PLMD::bias::ExtendedLagrangian, PLMD::ves::OutputFesBias, PLMD::isdb::JCoupling, PLMD::generic::Read, PLMD::generic::DumpMassCharge, PLMD::generic::Print, PLMD::isdb::PRE, PLMD::isdb::NOE, PLMD::generic::Flush, PLMD::generic::DumpDerivatives, PLMD::generic::DumpForces, PLMD::generic::DumpPDB, PLMD::generic::DumpProjections, PLMD::generic::PrintNDX, PLMD::generic::Accumulate, PLMD::generic::Collect, PLMD::generic::DumpVector, PLMD::contour::DumpContour, PLMD::logmfd::LogMFD, PLMD::eds::EDS, PLMD::fisst::FISST, PLMD::mapping::PathReparameterization, and PLMD::mapping::PathDisplacements.

◆ usingNaturalUnits()

bool PLMD::Action::usingNaturalUnits ( ) const
protectedinherited

Are we using natural units.

◆ 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_values = "%15.8f",
const std::string &  output_fmt_derivs = "%15.8f",
const bool  numerical_deriv = false 
) const

◆ writeInGraph()

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

Get the info on what to calculate.

Reimplemented in PLMD::generic::Print, PLMD::adjmat::ContactMatrix, PLMD::function::FunctionOfVector< T >, PLMD::function::FunctionOfMatrix< T >, PLMD::generic::PrintNDX, PLMD::function::FunctionOfScalar< T >, and PLMD::gridtools::FunctionOfGrid< T >.

Member Data Documentation

◆ action_pntr_

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

◆ 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.

◆ 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

◆ defaults

std::string PLMD::Action::defaults
privateinherited

The set of default arguments that we are using.

◆ description_

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

◆ doCheckPoint

bool PLMD::Action::doCheckPoint
privateinherited

◆ 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

◆ 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.

◆ log

Log& PLMD::Action::log
inherited

Reference to the log stream.

◆ multi_sim_comm

Communicator& PLMD::Action::multi_sim_comm
inherited

◆ name

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

Name of the directive in the plumed.dat file.

◆ nbasis_

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

◆ nbins_

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

◆ never_activate

bool PLMD::Action::never_activate
privateinherited

◆ norder_

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

◆ numerical_uniform_integrals_

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

◆ options

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

Option that you might have enabled.

◆ 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

◆ replica_index

int PLMD::Action::replica_index
privateinherited

◆ restart

bool PLMD::Action::restart
privateinherited

◆ timestep

double PLMD::Action::timestep
privateinherited

Save the timestep here.

◆ type_

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

◆ uniform_integrals_

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

◆ 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.

◆ vesbias_pntr_

VesBias* PLMD::ves::BasisFunctions::vesbias_pntr_
private
The documentation for this class was generated from the following files:
Hosted by GitHub   GitHub Logo doxygen 1.8.17