PLMD::ves::TD_ProductCombination Class Reference

Provides the keyword TD_PRODUCT_COMBINATION More...

Inheritance diagram for PLMD::ves::TD_ProductCombination:

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

Public Member Functions
	TD_ProductCombination (const ActionOptions &ao)
virtual void	activate ()
	Set action to active. More...
void	addDependency (Action *)
	Specify that this Action depends on another one. More...
void	allowBiasCutoff ()
void	apply () override
	Apply an Action. More...
virtual void	beforeUpdate ()
	Before Update. More...
bool	biasCutoffActive () const
bool	biasGridNeeded () const
bool	biasWithoutCutoffGridNeeded () const
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 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...
void	clearLogTargetDistGrid ()
virtual void	clearOptions ()
virtual void	deactivate ()
	Set action to inactive. More...
void	doNotAllowBiasCutoff ()
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...
bool	fesGridNeeded () const
void	fflush ()
	Tell to the Action to flush open files. More...
FILE *	fopen (const char *path, const char *mode)
	Opens a file. More...
bool	forcedNormalization () const
bool	getCPT () const
	Return true if we are doing at a checkpoint step. More...
const Dependencies &	getDependencies () const
	Return dependencies. More...
unsigned	getDimension () 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...
const std::string &	getLabel () const
	Returns the label. More...
Grid *	getLogTargetDistGridPntr () const
Grid	getMarginal (const std::vector< std::string > &)
const std::string &	getName () const
	Returns the name. More...
bool	getRestart () const
	Return true if we are doing a restart. More...
long int	getStep () const
	Return the present timestep. More...
Grid *	getTargetDistGridPntr () const
double	getTime () const
	Return the present time. More...
double	getTimeStep () const
	Return the timestep. More...
double	getValue (const std::vector< double > &) const override
bool	isActive () const
	Check if action is active. More...
bool	isBiasCutoffAllowed () const
bool	isDynamic () const
bool	isOptionOn (const std::string &s) const
	Check if an option is on. More...
bool	isStatic () const
bool	isTargetDistGridShiftedToZero () const
void	linkAction (Action *) override
void	linkBiasGrid (Grid *) override
void	linkBiasWithoutCutoffGrid (Grid *) override
void	linkFesGrid (Grid *) override
void	linkVesBias (VesBias *) override
virtual void	lockRequests ()
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...
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	readInRestartTargetDistGrid (const std::string &)
virtual void	runFinalJobs ()
	RunFinalJobs This method is called once at the very end of the calculation. More...
void	setDimension (const unsigned int dimension)
virtual void	setOption (const std::string &s)
void	setupBiasCutoff ()
void	setupGrids (const std::vector< Value * > &, const std::vector< std::string > &, const std::vector< std::string > &, const std::vector< unsigned int > &)
virtual void	unlockRequests ()
void	update () override
	Update. More...
void	updateGrid () override
void	updateTargetDist ()
void	warning (const std::string &msg)
	Issue a warning. More...

Static Public Member Functions
static Grid	getMarginalDistributionGrid (Grid *, const std::vector< std::string > &)
static double	integrateGrid (const Grid *)
static double	normalizeGrid (Grid *)
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	applyTargetDistModiferToGrid (TargetDistModifer *modifer_pntr)
double	getBeta () const
Grid *	getBiasGridPntr () const
Grid *	getBiasWithoutCutoffGridPntr () const
Grid *	getFesGridPntr () const
Action *	getPntrToAction () const
VesBias *	getPntrToVesBias () const
Grid &	logTargetDistGrid () const
void	normalizeTargetDistGrid ()
void	setBiasGridNeeded ()
void	setBiasWithoutCutoffGridNeeded ()
void	setDynamic ()
void	setFesGridNeeded ()
void	setForcedNormalization ()
void	setMinimumOfTargetDistGridToZero ()
void	setStatic ()
Grid &	targetDistGrid () const
void	unsetForcedNormalization ()
void	updateLogTargetDistGrid ()

Private Types
enum	TargetDistType { static_targetdist, dynamic_targetdist }

Private Member Functions
void	calculateStaticDistributionGrid ()
void	checkNanAndInf ()
void	setupAdditionalGrids (const std::vector< Value * > &, const std::vector< std::string > &, const std::vector< std::string > &, const std::vector< unsigned int > &) override
void	updateBiasCutoffForTargetDistGrid ()

Private Attributes
Action *	action_pntr_
bool	active
	Switch to activate Action on this step. More...
Dependencies	after
	Actions on which this Action depends. More...
bool	allow_bias_cutoff_
bool	bias_cutoff_active_
Grid *	bias_grid_pntr_
Grid *	bias_withoutcutoff_grid_pntr_
bool	check_nan_inf_
bool	check_nonnegative_
bool	check_normalization_
unsigned int	dimension_
std::vector< TargetDistribution * >	distribution_pntrs_
bool	doCheckPoint
Grid *	fes_grid_pntr_
bool	force_normalization_
std::vector< Value * >	grid_args_
std::vector< Grid * >	grid_pntrs_
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...
std::unique_ptr< Grid >	log_targetdist_grid_pntr_
const std::string	name
	Name of the directive in the plumed.dat file. More...
unsigned int	ndist_
bool	needs_bias_grid_
bool	needs_bias_withoutcutoff_grid_
bool	needs_fes_grid_
std::set< std::string >	options
	Option that you might have enabled. More...
int	replica_index
bool	restart
bool	shift_targetdist_to_zero_
bool	static_grid_calculated
std::unique_ptr< Grid >	targetdist_grid_pntr_
std::vector< std::unique_ptr< TargetDistModifer > >	targetdist_modifer_pntrs_
enum PLMD::ves::TargetDistribution::TargetDistType	type_
double	update_from
	Update only after this time. More...
double	update_until
	Update only until this time. More...
VesBias *	vesbias_pntr_

Detailed Description

Provides the keyword TD_PRODUCT_COMBINATION

Member Typedef Documentation

Dependencies

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

inherited

Member Enumeration Documentation

TargetDistType

enum PLMD::ves::TargetDistribution::TargetDistType

privateinherited

Enumerator
static_targetdist
dynamic_targetdist

Constructor & Destructor Documentation

TD_ProductCombination()

PLMD::ves::TD_ProductCombination::TD_ProductCombination ( 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.

allowBiasCutoff()

void PLMD::ves::TargetDistribution::allowBiasCutoff ( )

inlineinherited

apply()

void PLMD::ves::TargetDistribution::apply ( )

inlineoverridevirtualinherited

Apply an Action.

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

Implements PLMD::Action.

applyTargetDistModiferToGrid()

void PLMD::ves::TargetDistribution::applyTargetDistModiferToGrid ( TargetDistModifer *  modifer_pntr )

protectedinherited

beforeUpdate()

virtual void PLMD::Action::beforeUpdate ( )

inlinevirtualinherited

Before Update.

This is a special method that is called just before the update() method. It can be used by actions that want to do something irrespectively of the fact that update() is active or not. In other words, this is always called, even when action is not active.

Reimplemented in PLMD::generic::UpdateIf.

biasCutoffActive()

bool PLMD::ves::TargetDistribution::biasCutoffActive ( ) const

inlineinherited

biasGridNeeded()

bool PLMD::ves::TargetDistribution::biasGridNeeded ( ) const

inlineinherited

biasWithoutCutoffGridNeeded()

bool PLMD::ves::TargetDistribution::biasWithoutCutoffGridNeeded ( ) const

inlineinherited

calculate()

void PLMD::ves::TargetDistribution::calculate ( )

inlineoverridevirtualinherited

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

calculateStaticDistributionGrid()

void PLMD::ves::TargetDistribution::calculateStaticDistributionGrid ( )

privateinherited

checkNanAndInf()

void PLMD::ves::TargetDistribution::checkNanAndInf ( )

privateinherited

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.

clearLogTargetDistGrid()

void PLMD::ves::TargetDistribution::clearLogTargetDistGrid ( )

inherited

clearOptions()

void PLMD::Action::clearOptions ( )

virtualinherited

deactivate()

void PLMD::Action::deactivate ( )

inlinevirtualinherited

Set action to inactive.

doNotAllowBiasCutoff()

void PLMD::ves::TargetDistribution::doNotAllowBiasCutoff ( )

inlineinherited

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().

fesGridNeeded()

bool PLMD::ves::TargetDistribution::fesGridNeeded ( ) const

inlineinherited

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)

forcedNormalization()

bool PLMD::ves::TargetDistribution::forcedNormalization ( ) const

inlineinherited

getBeta()

double PLMD::ves::TargetDistribution::getBeta ( ) const

protectedinherited

getBiasGridPntr()

Grid* PLMD::ves::TargetDistribution::getBiasGridPntr ( ) const

inlineprotectedinherited

getBiasWithoutCutoffGridPntr()

Grid* PLMD::ves::TargetDistribution::getBiasWithoutCutoffGridPntr ( ) const

inlineprotectedinherited

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.

getDimension()

unsigned PLMD::ves::TargetDistribution::getDimension ( ) 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.

getFesGridPntr()

Grid* PLMD::ves::TargetDistribution::getFesGridPntr ( ) const

inlineprotectedinherited

getKeyword()

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

inherited

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

getLabel()

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

inlineinherited

Returns the label.

getLogTargetDistGridPntr()

Grid* PLMD::ves::TargetDistribution::getLogTargetDistGridPntr ( ) const

inlineinherited

getMarginal()

Grid PLMD::ves::TargetDistribution::getMarginal ( const std::vector< std::string > &  args )

inherited

getMarginalDistributionGrid()

Grid PLMD::ves::TargetDistribution::getMarginalDistributionGrid ( Grid *  grid_pntr, const std::vector< std::string > &  args  )

staticinherited

getName()

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

inlineinherited

Returns the name.

getPntrToAction()

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

inlineprotectedinherited

getPntrToVesBias()

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

inlineprotectedinherited

getRestart()

bool PLMD::Action::getRestart ( ) const

inlineinherited

Return true if we are doing a restart.

getStep()

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

inherited

Return the present timestep.

getTargetDistGridPntr()

Grid* PLMD::ves::TargetDistribution::getTargetDistGridPntr ( ) const

inlineinherited

getTime()

double PLMD::Action::getTime ( ) const

inherited

Return the present time.

getTimeStep()

double PLMD::Action::getTimeStep ( ) const

inherited

Return the timestep.

getValue()

double PLMD::ves::TD_ProductCombination::getValue ( const std::vector< double > &  argument ) const

overridevirtual

Implements PLMD::ves::TargetDistribution.

integrateGrid()

double PLMD::ves::TargetDistribution::integrateGrid ( const Grid *  grid_pntr )

staticinherited

isActive()

bool PLMD::Action::isActive ( ) const

inlineinherited

Check if action is active.

isBiasCutoffAllowed()

bool PLMD::ves::TargetDistribution::isBiasCutoffAllowed ( ) const

inlineinherited

isDynamic()

bool PLMD::ves::TargetDistribution::isDynamic ( ) const

inlineinherited

isOptionOn()

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

inlineinherited

Check if an option is on.

isStatic()

bool PLMD::ves::TargetDistribution::isStatic ( ) const

inlineinherited

isTargetDistGridShiftedToZero()

bool PLMD::ves::TargetDistribution::isTargetDistGridShiftedToZero ( ) const

inlineinherited

linkAction()

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

overridevirtual

Reimplemented from PLMD::ves::TargetDistribution.

linkBiasGrid()

void PLMD::ves::TD_ProductCombination::linkBiasGrid ( Grid *  bias_grid_pntr_in )

overridevirtual

Reimplemented from PLMD::ves::TargetDistribution.

linkBiasWithoutCutoffGrid()

void PLMD::ves::TD_ProductCombination::linkBiasWithoutCutoffGrid ( Grid *  bias_withoutcutoff_grid_pntr_in )

overridevirtual

Reimplemented from PLMD::ves::TargetDistribution.

linkFesGrid()

void PLMD::ves::TD_ProductCombination::linkFesGrid ( Grid *  fes_grid_pntr_in )

overridevirtual

Reimplemented from PLMD::ves::TargetDistribution.

linkVesBias()

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

overridevirtual

Reimplemented from PLMD::ves::TargetDistribution.

lockRequests()

virtual void PLMD::Action::lockRequests ( )

inlinevirtualinherited

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

logTargetDistGrid()

Grid& PLMD::ves::TargetDistribution::logTargetDistGrid ( ) const

inlineprotectedinherited

normalizeGrid()

double PLMD::ves::TargetDistribution::normalizeGrid ( Grid *  grid_pntr )

staticinherited

normalizeTargetDistGrid()

void PLMD::ves::TargetDistribution::normalizeTargetDistGrid ( )

inlineprotectedinherited

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

readAtomsFromPDB()

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.

readInRestartTargetDistGrid()

void PLMD::ves::TargetDistribution::readInRestartTargetDistGrid ( const std::string &  grid_fname )

inherited

registerKeywords()

void PLMD::ves::TD_ProductCombination::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.

setBiasGridNeeded()

void PLMD::ves::TargetDistribution::setBiasGridNeeded ( )

inlineprotectedinherited

setBiasWithoutCutoffGridNeeded()

void PLMD::ves::TargetDistribution::setBiasWithoutCutoffGridNeeded ( )

inlineprotectedinherited

setDimension()

void PLMD::ves::TargetDistribution::setDimension ( const unsigned int  dimension )

inherited

setDynamic()

void PLMD::ves::TargetDistribution::setDynamic ( )

inlineprotectedinherited

setFesGridNeeded()

void PLMD::ves::TargetDistribution::setFesGridNeeded ( )

inlineprotectedinherited

setForcedNormalization()

void PLMD::ves::TargetDistribution::setForcedNormalization ( )

inlineprotectedinherited

setMinimumOfTargetDistGridToZero()

void PLMD::ves::TargetDistribution::setMinimumOfTargetDistGridToZero ( )

protectedinherited

setOption()

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

virtualinherited

setStatic()

void PLMD::ves::TargetDistribution::setStatic ( )

inlineprotectedinherited

setupAdditionalGrids()

void PLMD::ves::TD_ProductCombination::setupAdditionalGrids ( const std::vector< Value * > &  arguments, const std::vector< std::string > &  min, const std::vector< std::string > &  max, const std::vector< unsigned int > &  nbins  )

overrideprivatevirtual

Reimplemented from PLMD::ves::TargetDistribution.

setupBiasCutoff()

void PLMD::ves::TargetDistribution::setupBiasCutoff ( )

inherited

setupGrids()

void PLMD::ves::TargetDistribution::setupGrids ( const std::vector< Value * > &  arguments, const std::vector< std::string > &  min, const std::vector< std::string > &  max, const std::vector< unsigned int > &  nbins  )

inherited

targetDistGrid()

Grid& PLMD::ves::TargetDistribution::targetDistGrid ( ) const

inlineprotectedinherited

unlockRequests()

virtual void PLMD::Action::unlockRequests ( )

inlinevirtualinherited

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

unsetForcedNormalization()

void PLMD::ves::TargetDistribution::unsetForcedNormalization ( )

inlineprotectedinherited

update()

void PLMD::ves::TargetDistribution::update ( )

inlineoverridevirtualinherited

Update.

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

Reimplemented from PLMD::Action.

updateBiasCutoffForTargetDistGrid()

void PLMD::ves::TargetDistribution::updateBiasCutoffForTargetDistGrid ( )

privateinherited

updateGrid()

void PLMD::ves::TD_ProductCombination::updateGrid ( )

overridevirtual

Reimplemented from PLMD::ves::TargetDistribution.

updateLogTargetDistGrid()

void PLMD::ves::TargetDistribution::updateLogTargetDistGrid ( )

protectedinherited

updateTargetDist()

void PLMD::ves::TargetDistribution::updateTargetDist ( )

inherited

warning()

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

inherited

Issue a warning.

Member Data Documentation

action_pntr_

Action* PLMD::ves::TargetDistribution::action_pntr_

privateinherited

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.

allow_bias_cutoff_

bool PLMD::ves::TargetDistribution::allow_bias_cutoff_

privateinherited

bias_cutoff_active_

bool PLMD::ves::TargetDistribution::bias_cutoff_active_

privateinherited

bias_grid_pntr_

Grid* PLMD::ves::TargetDistribution::bias_grid_pntr_

privateinherited

bias_withoutcutoff_grid_pntr_

Grid* PLMD::ves::TargetDistribution::bias_withoutcutoff_grid_pntr_

privateinherited

check_nan_inf_

bool PLMD::ves::TargetDistribution::check_nan_inf_

privateinherited

check_nonnegative_

bool PLMD::ves::TargetDistribution::check_nonnegative_

privateinherited

check_normalization_

bool PLMD::ves::TargetDistribution::check_normalization_

privateinherited

comm

Communicator& PLMD::Action::comm

inherited

dimension_

unsigned int PLMD::ves::TargetDistribution::dimension_

privateinherited

distribution_pntrs_

std::vector<TargetDistribution*> PLMD::ves::TD_ProductCombination::distribution_pntrs_

private

doCheckPoint

bool PLMD::Action::doCheckPoint

privateinherited

fes_grid_pntr_

Grid* PLMD::ves::TargetDistribution::fes_grid_pntr_

privateinherited

files

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

inherited

force_normalization_

bool PLMD::ves::TargetDistribution::force_normalization_

privateinherited

grid_args_

std::vector<Value*> PLMD::ves::TargetDistribution::grid_args_

privateinherited

grid_pntrs_

std::vector<Grid*> PLMD::ves::TD_ProductCombination::grid_pntrs_

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.

log_targetdist_grid_pntr_

std::unique_ptr<Grid> PLMD::ves::TargetDistribution::log_targetdist_grid_pntr_

privateinherited

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.

ndist_

unsigned int PLMD::ves::TD_ProductCombination::ndist_

private

needs_bias_grid_

bool PLMD::ves::TargetDistribution::needs_bias_grid_

privateinherited

needs_bias_withoutcutoff_grid_

bool PLMD::ves::TargetDistribution::needs_bias_withoutcutoff_grid_

privateinherited

needs_fes_grid_

bool PLMD::ves::TargetDistribution::needs_fes_grid_

privateinherited

options

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

privateinherited

Option that you might have enabled.

plumed

PlumedMain& PLMD::Action::plumed

inherited

Reference to main plumed object.

replica_index

int PLMD::Action::replica_index

privateinherited

restart

bool PLMD::Action::restart

privateinherited

shift_targetdist_to_zero_

bool PLMD::ves::TargetDistribution::shift_targetdist_to_zero_

privateinherited

static_grid_calculated

bool PLMD::ves::TargetDistribution::static_grid_calculated

privateinherited

targetdist_grid_pntr_

std::unique_ptr<Grid> PLMD::ves::TargetDistribution::targetdist_grid_pntr_

privateinherited

targetdist_modifer_pntrs_

std::vector<std::unique_ptr<TargetDistModifer> > PLMD::ves::TargetDistribution::targetdist_modifer_pntrs_

privateinherited

type_

enum PLMD::ves::TargetDistribution::TargetDistType PLMD::ves::TargetDistribution::type_

privateinherited

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::TargetDistribution::vesbias_pntr_

privateinherited

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

• ves/TD_ProductCombination.cpp