PLMD::ves::BF_Custom Class Reference

Provides the keyword BF_CUSTOM More...

Inheritance diagram for PLMD::ves::BF_Custom:

Public Types
typedef std::vector< Action * >	Dependencies

Public Member Functions
	BF_Custom (const ActionOptions &)
	~BF_Custom ()
virtual void	activate ()
	Set action to active. More...
void	addDependency (Action *)
	Specify that this Action depends on another one. More...
void	apply ()
	Apply an Action. More...
bool	arePeriodic () const
virtual void	beforeUpdate ()
	Before Update. More...
void	calculate ()
	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...
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...
void	getAllValues (const double, double &, bool &, std::vector< double > &, std::vector< double > &) const
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...
const Dependencies &	getDependencies () const
	Return dependencies. More...
std::string	getDescription () const
virtual std::string	getDocumentation () const
bool	getExchangeStep () const
	Check if we are on an exchange step. 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 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...
virtual void	runFinalJobs ()
	RunFinalJobs This method is called once at the very end of the calculation. More...
virtual void	setOption (const std::string &s)
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="%15.8f", const bool numerical_deriv=false) const

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
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)
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 ()

Private Attributes
std::vector< lepton::CompiledExpression >	bf_derivs_expressions_
std::vector< double * >	bf_derivs_lepton_ref_
std::vector< lepton::CompiledExpression >	bf_values_expressions_
std::vector< double * >	bf_values_lepton_ref_
bool	check_nan_inf_
bool	do_transf_
lepton::CompiledExpression	transf_deriv_expression_
double *	transf_deriv_lepton_ref_
lepton::CompiledExpression	transf_value_expression_
double *	transf_value_lepton_ref_
std::string	transf_variable_str_
std::string	variable_str_

Detailed Description

Provides the keyword BF_CUSTOM

Member Typedef Documentation

Dependencies

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

inherited

Constructor & Destructor Documentation

BF_Custom()

PLMD::ves::BF_Custom::BF_Custom ( const ActionOptions &  ao )

explicit

~BF_Custom()

PLMD::ves::BF_Custom::~BF_Custom ( )

inline

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  )

protectedinherited

addKeywordToList() [2/3]

template<typename T >

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

protectedinherited

addKeywordToList() [3/3]

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

inlineprotectedinherited

apply()

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

inlinevirtualinherited

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

inlineinherited

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 ( )

inlinevirtualinherited

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::ActionAtomistic, PLMD::multicolvar::MultiColvarBase, PLMD::analysis::AnalysisBase, PLMD::vesselbase::ActionWithAveraging, PLMD::mapping::Mapping, PLMD::multicolvar::DumpMultiColvar, PLMD::ActionWithArguments, PLMD::multicolvar::BridgedMultiColvarFunction, and PLMD::vesselbase::ActionWithInputVessel.

checkIfArgumentInsideInterval()

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

inlineinherited

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()

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

virtual

Implements PLMD::ves::BasisFunctions.

getBasisFunctionLabel()

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

inlineinherited

getBasisFunctionLabels()

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

inlineinherited

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

inlineinherited

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

inlineinherited

getKeywordString()

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

inherited

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

inherited

getName()

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

inlineinherited

Returns the name.

getNumberOfBasisFunctions()

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

inlineinherited

getOrder()

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

inlineinherited

getPntrToAction()

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

inlineinherited

getPntrToVesBias()

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

inlineinherited

getRestart()

bool PLMD::Action::getRestart ( ) const

inlineinherited

Return true if we are doing a restart.

getSize()

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

inlineinherited

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

inherited

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

inlineinherited

getUniformIntegrals()

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

inlineinherited

getValue()

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

inherited

hasBeenSet()

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

inlineinherited

intervalBounded()

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

inlineinherited

intervalDerivf()

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

inlineinherited

intervalMax()

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

inlineinherited

intervalMaxStr()

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

inlineinherited

intervalMean()

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

inlineinherited

intervalMin()

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

inlineinherited

intervalMinStr()

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

inlineinherited

intervalRange()

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

inlineinherited

intrinsicIntervalMax()

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

inlineprotectedinherited

intrinsicIntervalMaxStr()

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

inlineprotectedinherited

intrinsicIntervalMin()

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

inlineprotectedinherited

intrinsicIntervalMinStr()

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

inlineprotectedinherited

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 )

inherited

linkVesBias()

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

inherited

lockRequests()

virtual void PLMD::Action::lockRequests ( )

inlinevirtualinherited

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

numberOfBasisFunctions()

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

inlineinherited

numericalTargetDistributionIntegralsFromGrid()

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

protectedinherited

numericalUniformIntegrals()

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

protectedinherited

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::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.

printInfo()

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

inherited

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

setAllUniformIntegralsToZero()

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

inlineprotectedinherited

setDescription()

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

inlineprotectedinherited

setInterval() [1/2]

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

protectedinherited

setInterval() [2/2]

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

protectedinherited

setIntervalBounded()

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

inlineprotectedinherited

setIntervalNonBounded()

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

inlineprotectedinherited

setIntrinsicInterval() [1/2]

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

protectedinherited

setIntrinsicInterval() [2/2]

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

protectedinherited

setLabel()

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

inlineprotectedinherited

setLabelPrefix()

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

inlineprotectedinherited

setLabels()

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

inlineprotectedinherited

setNonPeriodic()

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

inlineprotectedinherited

setNumberOfBasisFunctions()

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

inlineprotectedinherited

setNumericalIntegrationBins()

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

inlineprotectedinherited

setOption()

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

virtualinherited

setOrder()

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

inlineprotectedinherited

setPeriodic()

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

inlineprotectedinherited

setType()

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

inlineprotectedinherited

setUniformIntegral()

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

inlineprotectedinherited

setUniformIntegrals()

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

inlineprotectedinherited

setupBF()

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

protectedinherited

setupInterval()

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

protectedinherited

setupLabels()

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

protectedvirtualinherited

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 ( )

protectedvirtualinherited

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

inlineinherited

unlockRequests()

virtual void PLMD::Action::unlockRequests ( )

inlinevirtualinherited

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

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::logmfd::LogMFD, PLMD::ves::VesLinearExpansion, PLMD::bias::PBMetaD, PLMD::isdb::Metainference, PLMD::eds::EDS, PLMD::ves::Optimizer, PLMD::isdb::RDC, PLMD::ves::TargetDistribution, PLMD::bias::MaxEnt, PLMD::generic::Plumed, PLMD::generic::DumpAtoms, PLMD::isdb::SAXS, PLMD::bias::ExtendedLagrangian, PLMD::multicolvar::VolumeTetrapore, PLMD::multicolvar::VolumeCavity, PLMD::generic::EffectiveEnergyDrift, PLMD::mapping::AdaptivePath, PLMD::generic::DumpMassCharge, PLMD::isdb::JCoupling, PLMD::generic::Read, PLMD::analysis::AnalysisBase, PLMD::generic::Print, PLMD::ves::OutputFesBias, PLMD::isdb::PRE, PLMD::vesselbase::ActionWithAveraging, PLMD::adjmat::OutputCluster, PLMD::isdb::NOE, PLMD::multicolvar::DumpMultiColvar, PLMD::generic::Flush, PLMD::generic::DumpDerivatives, PLMD::analysis::ReadDissimilarityMatrix, PLMD::generic::DumpForces, PLMD::generic::DumpProjections, PLMD::adjmat::DumpGraph, PLMD::analysis::ReadAnalysisFrames, 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

inherited

Member Data Documentation

bf_derivs_expressions_

std::vector<lepton::CompiledExpression> PLMD::ves::BF_Custom::bf_derivs_expressions_

private

bf_derivs_lepton_ref_

std::vector<double*> PLMD::ves::BF_Custom::bf_derivs_lepton_ref_

private

bf_values_expressions_

std::vector<lepton::CompiledExpression> PLMD::ves::BF_Custom::bf_values_expressions_

private

bf_values_lepton_ref_

std::vector<double*> PLMD::ves::BF_Custom::bf_values_lepton_ref_

private

check_nan_inf_

bool PLMD::ves::BF_Custom::check_nan_inf_

private

comm

Communicator& PLMD::Action::comm

inherited

do_transf_

bool PLMD::ves::BF_Custom::do_transf_

private

files

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

inherited

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

plumed

PlumedMain& PLMD::Action::plumed

inherited

Reference to main plumed object.

transf_deriv_expression_

lepton::CompiledExpression PLMD::ves::BF_Custom::transf_deriv_expression_

private

transf_deriv_lepton_ref_

double* PLMD::ves::BF_Custom::transf_deriv_lepton_ref_

private

transf_value_expression_

lepton::CompiledExpression PLMD::ves::BF_Custom::transf_value_expression_

private

transf_value_lepton_ref_

double* PLMD::ves::BF_Custom::transf_value_lepton_ref_

private

transf_variable_str_

std::string PLMD::ves::BF_Custom::transf_variable_str_

private

variable_str_

std::string PLMD::ves::BF_Custom::variable_str_

private

---

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

• ves/BF_Custom.cpp