PLMD::ves::Opt_Dummy Class Reference

Provides the keyword OPT_DUMMY More...

Inheritance diagram for PLMD::ves::Opt_Dummy:

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

Public Member Functions
	Opt_Dummy (const ActionOptions &)
void	coeffsUpdate (const unsigned int c_id=0)
std::string	getType () const
std::string	getDescription () const
unsigned int	numberOfBiases () const
unsigned int	numberOfCoeffsSets () const
std::vector< double >	getStepSizes () const
std::vector< double >	getCurrentStepSizes () const
double	getStepSize (const unsigned int coeffs_id=0) const
double	getCurrentStepSize (const unsigned int coeffs_id=0) const
void	setStepSizes (const std::vector< double > &)
void	setStepSize (const double, const unsigned int coeffs_id=0)
unsigned int	getIterationCounter () const
double	getIterationCounterDbl () const
std::string	getIterationCounterStr (const int offset=0) const
void	setIterationCounter (const unsigned int)
void	increaseIterationCounter ()
void	apply ()
	Apply an Action. More...
void	calculate ()
	Calculate an Action. More...
void	update ()
	Update. More...
unsigned int	getNumberOfDerivatives ()
bool	fixedStepSize () const
bool	dynamicStepSize () const
bool	useHessian () const
bool	diagonalHessian () const
bool	useMultipleWalkers () const
std::vector< VesBias * >	getBiasPntrs () const
std::vector< CoeffsVector * >	getCoeffsPntrs () const
std::vector< CoeffsVector * >	getAuxCoeffsPntrs () const
std::vector< CoeffsVector * >	getGradientPntrs () const
std::vector< CoeffsMatrix * >	getHessianPntrs () const
std::vector< CoeffsVector * >	getCoeffsMaskPntrs () const
std::vector< CoeffsVector * >	getTargetDistAveragesPntrs () const
bool	isBiasOutputActive () const
unsigned int	getBiasOutputStride () const
void	setBiasOutputStride (unsigned int stride)
void	writeBiasOutputFiles () const
bool	isFesOutputActive () const
unsigned int	getFesOutputStride () const
void	setFesOutputStride (unsigned int stride)
void	writeFesOutputFiles () const
bool	isFesProjOutputActive () const
unsigned int	getFesProjOutputStride () const
void	setFesProjOutputStride (unsigned int stride)
void	writeFesProjOutputFiles () const
bool	isTargetDistOutputActive () const
unsigned int	getTargetDistOutputStride () const
void	setTargetDistOutputStride (unsigned int stride)
void	writeTargetDistOutputFiles () const
bool	isTargetDistProjOutputActive () const
unsigned int	getTargetDistProjOutputStride () const
void	setTargetDistProjOutputStride (unsigned int stride)
void	writeTargetDistProjOutputFiles () const
virtual bool	onStep () const
	Check if the action is active on this step. More...
void	setStride (const int &n)
	Set the value of the stride. More...
int	getStride () const
	Get the stride. More...
bool	checkUpdate () const
	Check if action should be updated. More...
void	addDependency (Action *)
	Specify that this Action depends on another one. More...
void	clearDependencies ()
	Clear the dependence list for this Action. More...
long int	getStep () const
	Return the present timestep. More...
double	getTime () const
	Return the present time. More...
double	getTimeStep () const
	Return the timestep. More...
bool	getRestart () const
	Return true if we are doing a restart. More...
bool	getCPT () const
	Return true if we are doing at a checkpoint step. More...
std::string	getKeyword (const std::string &key)
	Just read one of the keywords and return the whole thing as a string. More...
template<class T >
void	parse (const std::string &key, T &t)
	Parse one keyword as generic type. More...
template<class T >
bool	parseNumbered (const std::string &key, const int no, T &t)
	Parse one numbered keyword as generic type. More...
template<class T >
void	parseVector (const std::string &key, std::vector< T > &t)
	Parse one keyword as std::vector. More...
template<class T >
bool	parseNumberedVector (const std::string &key, const int no, std::vector< T > &t)
	Parse a vector with a number. More...
void	parseFlag (const std::string &key, bool &t)
	Parse one keyword as boolean flag. More...
void	error (const std::string &msg) const
	Crash calculation and print documentation. More...
void	warning (const std::string &msg)
	Issue a warning. More...
void	exit (int c=0)
	Exit with error code c. More...
void	checkRead ()
	Check if Action was properly read. More...
virtual void	prepare ()
	Prepare an Action for calculation This can be used by Action if they need some special preparation before calculation. More...
virtual void	lockRequests ()
virtual void	unlockRequests ()
virtual void	beforeUpdate ()
	Before Update. More...
virtual void	runFinalJobs ()
	RunFinalJobs This method is called once at the very end of the calculation. More...
void	fflush ()
	Tell to the Action to flush open files. More...
virtual std::string	getDocumentation () const
const std::string &	getLabel () const
	Returns the label. More...
const std::string &	getName () const
	Returns the name. More...
virtual void	activate ()
	Set action to active. More...
virtual void	setOption (const std::string &s)
virtual void	clearOptions ()
virtual void	deactivate ()
	Set action to inactive. More...
bool	isActive () const
	Check if action is active. More...
bool	isOptionOn (const std::string &s) const
	Check if an option is on. More...
const Dependencies &	getDependencies () const
	Return dependencies. More...
virtual bool	checkNumericalDerivatives () const
	Check if numerical derivatives should be performed. More...
bool	checkNumericalDerivatives () const
	Check if numerical derivatives should be used. More...
virtual bool	checkNeedsGradients () const
	Check if the action needs gradient. More...
virtual void	calculateNumericalDerivatives (ActionWithValue *a=NULL)
	Perform calculation using numerical derivatives N.B. More...
FILE *	fopen (const char *path, const char *mode)
	Opens a file. More...
int	fclose (FILE *fp)
	Closes a file opened with Action::fclose(). More...
void	calculateFromPDB (const PDB &)
	Calculate the action given a pdb file as input. More...
virtual void	readAtomsFromPDB (const PDB &)
	This is overwritten in ActionAtomistic so that we can read the atoms from the pdb input file rather than taking them from the MD code. More...
bool	getExchangeStep () const
	Check if we are on an exchange step. More...
std::string	cite (const std::string &s)
	Cite a paper see PlumedMain::cite. More...
void	addValue ()
	Add a value with the name label. More...
void	addValueWithDerivatives ()
	Add a value with the name label that has derivatives. More...
void	setNotPeriodic ()
	Set your default value to have no periodicity. More...
void	setPeriodic (const std::string &min, const std::string &max)
	Set the value to be periodic with a particular domain. More...
void	setValue (Value *, double)
	Set the value. More...
void	addComponent (const std::string &name)
	Add a value with a name like label.name. More...
void	addComponentWithDerivatives (const std::string &name)
	Add a value with a name like label.name that has derivatives. More...
void	componentIsNotPeriodic (const std::string &name)
	Set your value component to have no periodicity. More...
void	componentIsPeriodic (const std::string &name, const std::string &min, const std::string &max)
	Set the value to be periodic with a particular domain. More...
virtual bool	doNotCalculateDerivatives () const
	Are we not calculating derivatives. More...
double	getOutputQuantity (const unsigned j) const
	Get the value of one of the components of the PLMD::Action. More...
double	getOutputQuantity (const std::string &name) const
	Get the value with a specific name (N.B. if there is no such value this returns zero) More...
bool	exists (const std::string &name) const
	Check if a value with a particular name is present. More...
Value *	copyOutput (const std::string &name) const
	Return a pointer to the value with name (this is used to retrieve values in other PLMD::Actions) You should NEVER use this routine to refer to the components of your PLMD::Action. More...
Value *	copyOutput (const unsigned &n) const
	Return a pointer to the value with this number (this is used to retrieve values in other PLMD::Actions) You should NEVER use this routine to refer to the components of your PLMD::Action. More...
std::string	getComponentsList () const
	get a string that contains all the available components More...
std::vector< std::string >	getComponentsVector () const
	get a vector that contains the label for all the components More...
int	getNumberOfComponents () const
	Returns the number of values defined. More...
void	clearInputForces ()
	Clear the forces on the values. More...
virtual void	clearDerivatives ()
	Clear the derivatives of values wrt parameters. More...
void	setGradientsIfNeeded ()
	Calculate the gradients and store them for all the values (need for projections) More...
void	useNumericalDerivatives ()
	This forces the class to use numerical derivatives. More...
virtual void	checkFieldsAllowed ()
virtual void	turnOnDerivatives ()
	Activate the calculation of derivatives. More...

Static Public Member Functions
static void	registerKeywords (Keywords &)
static void	useMultipleWalkersKeywords (Keywords &)
static void	useHessianKeywords (Keywords &)
static void	useFixedStepSizeKeywords (Keywords &)
static void	useDynamicStepSizeKeywords (Keywords &)
static void	useMaskKeywords (Keywords &)
static void	useRestartKeywords (Keywords &)
static void	useMonitorAverageGradientKeywords (Keywords &)
static void	useDynamicTargetDistributionKeywords (Keywords &)
static void	useReweightFactorKeywords (Keywords &)
static void	noAnalyticalDerivatives (Keywords &keys)
	Insist that numerical derivatives should always be used for an action and make this fact appear in the manual. More...
static void	componentsAreNotOptional (Keywords &keys)
	Puts a message into the manual that the components always output. More...
static void	useCustomisableComponents (Keywords &keys)
	The components in the action will depend on the user. More...

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

Protected Member Functions
void	turnOnHessian ()
void	turnOffHessian ()
std::vector< CoeffsMatrix * >	enableHessian (VesBias *, const bool diagonal_hessian=false)
CoeffsVector &	Coeffs (const unsigned int coeffs_id=0) const
CoeffsVector &	AuxCoeffs (const unsigned int coeffs_id=0) const
CoeffsVector &	Gradient (const unsigned int coeffs_id=0) const
CoeffsMatrix &	Hessian (const unsigned int coeffs_id=0) const
CoeffsVector &	CoeffsMask (const unsigned int coeffs_id=0) const
CoeffsVector &	TargetDistAverages (const unsigned int coeffs_id=0) const
double	StepSize (const unsigned int coeffs_id=0) const
void	setCurrentStepSize (const double, const unsigned int i=0)
void	setCurrentStepSizes (const std::vector< double > &)
void	turnOffCoeffsOutputFiles ()
template<class T >
bool	parseMultipleValues (const std::string &, std::vector< T > &)
template<class T >
bool	parseMultipleValues (const std::string &, std::vector< T > &, const T &)
void	parseFilenames (const std::string &, std::vector< std::string > &, const std::string &)
void	parseFilenames (const std::string &, std::vector< std::string > &)
void	addCoeffsSetIDsToFilenames (std::vector< std::string > &, std::string &)
void	setupOFiles (std::vector< std::string > &, std::vector< OFile *> &, const bool multi_sim_single_files=false)
Value *	getPntrToValue ()
	Get a pointer to the default value. More...
void	setValue (const double &d)
	Set the default value (the one without name) More...
Value *	getPntrToComponent (int i)
	Return a pointer to the component by index. More...
Value *	getPntrToComponent (const std::string &name)
	Return a pointer to the value by name. More...

Detailed Description

Provides the keyword OPT_DUMMY

Member Typedef Documentation

Dependencies

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

inherited

Constructor & Destructor Documentation

Opt_Dummy()

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

explicit

Member Function Documentation

activate()

void PLMD::Action::activate ( )

virtualinherited

Set action to active.

addCoeffsSetIDsToFilenames()

void PLMD::ves::Optimizer::addCoeffsSetIDsToFilenames ( std::vector< std::string > &  fnames, std::string &  coeffssetid_prefix  )

protectedinherited

addComponent()

void PLMD::ActionWithValue::addComponent ( const std::string &  name )

inherited

Add a value with a name like label.name.

addComponentWithDerivatives()

void PLMD::ActionWithValue::addComponentWithDerivatives ( const std::string &  name )

inherited

Add a value with a name like label.name that has derivatives.

addDependency()

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

inherited

Specify that this Action depends on another one.

addValue()

void PLMD::ActionWithValue::addValue ( )

inherited

Add a value with the name label.

addValueWithDerivatives()

void PLMD::ActionWithValue::addValueWithDerivatives ( )

inherited

Add a value with the name label that has derivatives.

apply()

void PLMD::ves::Optimizer::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.

AuxCoeffs()

CoeffsVector & PLMD::ves::Optimizer::AuxCoeffs ( const unsigned int  coeffs_id = 0 ) const

inlineprotectedinherited

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

checkFieldsAllowed()

virtual void PLMD::ActionWithValue::checkFieldsAllowed ( )

inlinevirtualinherited

Reimplemented in PLMD::colvar::ContactMap.

checkNeedsGradients()

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

inlinevirtualinherited

Check if the action needs gradient.

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

checkNumericalDerivatives() [1/2]

bool PLMD::ActionWithValue::checkNumericalDerivatives ( ) const

inlinevirtualinherited

Check if numerical derivatives should be used.

Reimplemented from PLMD::Action.

checkNumericalDerivatives() [2/2]

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

inlinevirtualinherited

Check if numerical derivatives should be performed.

Reimplemented in PLMD::ActionWithValue.

checkRead()

void PLMD::Action::checkRead ( )

inherited

Check if Action was properly read.

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

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.

clearDerivatives()

void PLMD::ActionWithValue::clearDerivatives ( )

virtualinherited

Clear the derivatives of values wrt parameters.

Reimplemented in PLMD::multicolvar::BridgedMultiColvarFunction, and PLMD::manyrestraints::ManyRestraintsBase.

clearInputForces()

void PLMD::ActionWithValue::clearInputForces ( )

inherited

Clear the forces on the values.

clearOptions()

void PLMD::Action::clearOptions ( )

virtualinherited

Coeffs()

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

inlineprotectedinherited

CoeffsMask()

CoeffsVector & PLMD::ves::Optimizer::CoeffsMask ( const unsigned int  coeffs_id = 0 ) const

inlineprotectedinherited

coeffsUpdate()

void PLMD::ves::Opt_Dummy::coeffsUpdate ( const unsigned int  c_id = 0 )

virtual

Implements PLMD::ves::Optimizer.

componentIsNotPeriodic()

void PLMD::ActionWithValue::componentIsNotPeriodic ( const std::string &  name )

inherited

Set your value component to have no periodicity.

componentIsPeriodic()

void PLMD::ActionWithValue::componentIsPeriodic ( const std::string &  name, const std::string &  min, const std::string &  max  )

inherited

Set the value to be periodic with a particular domain.

componentsAreNotOptional()

void PLMD::ActionWithValue::componentsAreNotOptional ( Keywords &  keys )

staticinherited

Puts a message into the manual that the components always output.

copyOutput() [1/2]

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

inherited

Return a pointer to the value with name (this is used to retrieve values in other PLMD::Actions) You should NEVER use this routine to refer to the components of your PLMD::Action.

Use getPntrToComponent instead.

copyOutput() [2/2]

Value * PLMD::ActionWithValue::copyOutput ( const unsigned &  n ) const

inherited

Return a pointer to the value with this number (this is used to retrieve values in other PLMD::Actions) You should NEVER use this routine to refer to the components of your PLMD::Action.

Use getPntrToComponent instead.

deactivate()

void PLMD::Action::deactivate ( )

inlinevirtualinherited

Set action to inactive.

diagonalHessian()

bool PLMD::ves::Optimizer::diagonalHessian ( ) const

inlineinherited

doNotCalculateDerivatives()

bool PLMD::ActionWithValue::doNotCalculateDerivatives ( ) const

inlinevirtualinherited

Are we not calculating derivatives.

Reimplemented in PLMD::multicolvar::MultiColvarBase.

dynamicStepSize()

bool PLMD::ves::Optimizer::dynamicStepSize ( ) const

inlineinherited

enableHessian()

std::vector< CoeffsMatrix * > PLMD::ves::Optimizer::enableHessian ( VesBias *  bias_pntr_in, const bool  diagonal_hessian = false  )

protectedinherited

error()

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

inherited

Crash calculation and print documentation.

exists()

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

inherited

Check if a value with a particular name is present.

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

exit()

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

inherited

Exit with error code c.

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.

fixedStepSize()

bool PLMD::ves::Optimizer::fixedStepSize ( ) const

inlineinherited

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)

getAuxCoeffsPntrs()

std::vector<CoeffsVector*> PLMD::ves::Optimizer::getAuxCoeffsPntrs ( ) const

inlineinherited

getBiasOutputStride()

unsigned int PLMD::ves::Optimizer::getBiasOutputStride ( ) const

inlineinherited

getBiasPntrs()

std::vector<VesBias*> PLMD::ves::Optimizer::getBiasPntrs ( ) const

inlineinherited

getCoeffsMaskPntrs()

std::vector<CoeffsVector*> PLMD::ves::Optimizer::getCoeffsMaskPntrs ( ) const

inlineinherited

getCoeffsPntrs()

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

inlineinherited

getComponentsList()

std::string PLMD::ActionWithValue::getComponentsList ( ) const

inherited

get a string that contains all the available components

getComponentsVector()

std::vector< std::string > PLMD::ActionWithValue::getComponentsVector ( ) const

inherited

get a vector that contains the label for all the components

getCPT()

bool PLMD::Action::getCPT ( ) const

inherited

Return true if we are doing at a checkpoint step.

getCurrentStepSize()

double PLMD::ves::Optimizer::getCurrentStepSize ( const unsigned int  coeffs_id = 0 ) const

inlineinherited

getCurrentStepSizes()

std::vector< double > PLMD::ves::Optimizer::getCurrentStepSizes ( ) const

inlineinherited

getDependencies()

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

inlineinherited

Return dependencies.

getDescription()

std::string PLMD::ves::Optimizer::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.

getFesOutputStride()

unsigned int PLMD::ves::Optimizer::getFesOutputStride ( ) const

inlineinherited

getFesProjOutputStride()

unsigned int PLMD::ves::Optimizer::getFesProjOutputStride ( ) const

inlineinherited

getGradientPntrs()

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

inlineinherited

getHessianPntrs()

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

inlineinherited

getIterationCounter()

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

inlineinherited

getIterationCounterDbl()

double PLMD::ves::Optimizer::getIterationCounterDbl ( ) const

inlineinherited

getIterationCounterStr()

std::string PLMD::ves::Optimizer::getIterationCounterStr ( const int  offset = 0 ) const

inherited

getKeyword()

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

inherited

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

getLabel()

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

inlineinherited

Returns the label.

getName()

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

inlineinherited

Returns the name.

getNumberOfComponents()

int PLMD::ActionWithValue::getNumberOfComponents ( ) const

inlineinherited

Returns the number of values defined.

getNumberOfDerivatives()

unsigned int PLMD::ves::Optimizer::getNumberOfDerivatives ( )

inlinevirtualinherited

Implements PLMD::ActionWithValue.

getOutputQuantity() [1/2]

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

inlineinherited

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

getOutputQuantity() [2/2]

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

inlineinherited

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

getPntrToComponent() [1/2]

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

protectedinherited

Return a pointer to the component by index.

getPntrToComponent() [2/2]

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

protectedinherited

Return a pointer to the value by name.

getPntrToValue()

Value * PLMD::ActionWithValue::getPntrToValue ( )

protectedinherited

Get a pointer to the default value.

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.

getStepSize()

double PLMD::ves::Optimizer::getStepSize ( const unsigned int  coeffs_id = 0 ) const

inlineinherited

getStepSizes()

std::vector< double > PLMD::ves::Optimizer::getStepSizes ( ) const

inlineinherited

getStride()

int PLMD::ActionPilot::getStride ( ) const

inherited

Get the stride.

getTargetDistAveragesPntrs()

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

inlineinherited

getTargetDistOutputStride()

unsigned int PLMD::ves::Optimizer::getTargetDistOutputStride ( ) const

inlineinherited

getTargetDistProjOutputStride()

unsigned int PLMD::ves::Optimizer::getTargetDistProjOutputStride ( ) const

inlineinherited

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::Optimizer::getType ( ) const

inlineinherited

Gradient()

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

inlineprotectedinherited

Hessian()

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

inlineprotectedinherited

increaseIterationCounter()

void PLMD::ves::Optimizer::increaseIterationCounter ( )

inlineinherited

isActive()

bool PLMD::Action::isActive ( ) const

inlineinherited

Check if action is active.

isBiasOutputActive()

bool PLMD::ves::Optimizer::isBiasOutputActive ( ) const

inlineinherited

isFesOutputActive()

bool PLMD::ves::Optimizer::isFesOutputActive ( ) const

inlineinherited

isFesProjOutputActive()

bool PLMD::ves::Optimizer::isFesProjOutputActive ( ) const

inlineinherited

isOptionOn()

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

inlineinherited

Check if an option is on.

isTargetDistOutputActive()

bool PLMD::ves::Optimizer::isTargetDistOutputActive ( ) const

inlineinherited

isTargetDistProjOutputActive()

bool PLMD::ves::Optimizer::isTargetDistProjOutputActive ( ) const

inlineinherited

lockRequests()

virtual void PLMD::Action::lockRequests ( )

inlinevirtualinherited

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

noAnalyticalDerivatives()

void PLMD::ActionWithValue::noAnalyticalDerivatives ( Keywords &  keys )

staticinherited

Insist that numerical derivatives should always be used for an action and make this fact appear in the manual.

numberOfBiases()

unsigned int PLMD::ves::Optimizer::numberOfBiases ( ) const

inlineinherited

numberOfCoeffsSets()

unsigned int PLMD::ves::Optimizer::numberOfCoeffsSets ( ) const

inlineinherited

onStep()

bool PLMD::ActionPilot::onStep ( ) const

virtualinherited

Check if the action is active on this step.

Reimplemented in PLMD::gridtools::ConvertToFES.

parse()

template<class T >

void PLMD::Action::parse ( const std::string &  key, T &  t  )

inherited

Parse one keyword as generic type.

parseFilenames() [1/2]

void PLMD::ves::Optimizer::parseFilenames ( const std::string &  keyword, std::vector< std::string > &  fnames, const std::string &  default_fname  )

inlineprotectedinherited

parseFilenames() [2/2]

void PLMD::ves::Optimizer::parseFilenames ( const std::string &  keyword, std::vector< std::string > &  fnames  )

inlineprotectedinherited

parseFlag()

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

inherited

Parse one keyword as boolean flag.

parseMultipleValues() [1/2]

template<class T >

bool PLMD::ves::Optimizer::parseMultipleValues ( const std::string &  keyword, std::vector< T > &  values  )

protectedinherited

parseMultipleValues() [2/2]

template<class T >

bool PLMD::ves::Optimizer::parseMultipleValues ( const std::string &  keyword, std::vector< T > &  values, const T &  default_value  )

protectedinherited

parseNumbered()

template<class T >

bool PLMD::Action::parseNumbered ( const std::string &  key, const int  no, T &  t  )

inherited

Parse one numbered keyword as generic type.

parseNumberedVector()

template<class T >

bool PLMD::Action::parseNumberedVector ( const std::string &  key, const int  no, std::vector< T > &  t  )

inherited

Parse a vector with a number.

parseVector()

template<class T >

void PLMD::Action::parseVector ( const std::string &  key, std::vector< T > &  t  )

inherited

Parse one keyword as std::vector.

prepare()

void PLMD::Action::prepare ( )

virtualinherited

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

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

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

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::Opt_Dummy::registerKeywords ( Keywords &  keys )

static

runFinalJobs()

virtual void PLMD::Action::runFinalJobs ( )

inlinevirtualinherited

RunFinalJobs This method is called once at the very end of the calculation.

The set of all Actions in run for the final time in forward order.

Reimplemented in PLMD::analysis::Analysis, PLMD::gridtools::ConvertToFES, and PLMD::gridtools::GridPrintingBase.

setBiasOutputStride()

void PLMD::ves::Optimizer::setBiasOutputStride ( unsigned int  stride )

inlineinherited

setCurrentStepSize()

void PLMD::ves::Optimizer::setCurrentStepSize ( const double  current_stepsize_in, const unsigned int  i = 0  )

inlineprotectedinherited

setCurrentStepSizes()

void PLMD::ves::Optimizer::setCurrentStepSizes ( const std::vector< double > &  current_stepsizes_in )

inlineprotectedinherited

setFesOutputStride()

void PLMD::ves::Optimizer::setFesOutputStride ( unsigned int  stride )

inlineinherited

setFesProjOutputStride()

void PLMD::ves::Optimizer::setFesProjOutputStride ( unsigned int  stride )

inlineinherited

setGradientsIfNeeded()

void PLMD::ActionWithValue::setGradientsIfNeeded ( )

inherited

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

setIterationCounter()

void PLMD::ves::Optimizer::setIterationCounter ( const unsigned int  iter_counter_in )

inlineinherited

setNotPeriodic()

void PLMD::ActionWithValue::setNotPeriodic ( )

inherited

Set your default value to have no periodicity.

setOption()

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

virtualinherited

setPeriodic()

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

inherited

Set the value to be periodic with a particular domain.

setStepSize()

void PLMD::ves::Optimizer::setStepSize ( const double  stepsize_in, const unsigned int  coeffs_id = 0  )

inlineinherited

setStepSizes()

void PLMD::ves::Optimizer::setStepSizes ( const std::vector< double > &  stepsizes_in )

inlineinherited

setStride()

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

inherited

Set the value of the stride.

setTargetDistOutputStride()

void PLMD::ves::Optimizer::setTargetDistOutputStride ( unsigned int  stride )

inlineinherited

setTargetDistProjOutputStride()

void PLMD::ves::Optimizer::setTargetDistProjOutputStride ( unsigned int  stride )

inlineinherited

setupOFiles()

void PLMD::ves::Optimizer::setupOFiles ( std::vector< std::string > &  fnames, std::vector< OFile *> &  OFiles, const bool  multi_sim_single_files = false  )

protectedinherited

setValue() [1/2]

void PLMD::ActionWithValue::setValue ( const double &  d )

inlineprotectedinherited

Set the default value (the one without name)

setValue() [2/2]

void PLMD::ActionWithValue::setValue ( Value *  , double    )

inherited

Set the value.

StepSize()

double PLMD::ves::Optimizer::StepSize ( const unsigned int  coeffs_id = 0 ) const

inlineprotectedinherited

TargetDistAverages()

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

protectedinherited

turnOffCoeffsOutputFiles()

void PLMD::ves::Optimizer::turnOffCoeffsOutputFiles ( )

protectedinherited

turnOffHessian()

void PLMD::ves::Optimizer::turnOffHessian ( )

protectedinherited

turnOnDerivatives()

void PLMD::ActionWithValue::turnOnDerivatives ( )

virtualinherited

Activate the calculation of derivatives.

Reimplemented in PLMD::analysis::Histogram, PLMD::isdb::MetainferenceBase, PLMD::eds::EDS, PLMD::multicolvar::MultiColvarBase, PLMD::generic::Read, PLMD::adjmat::ClusterDiameter, PLMD::secondarystructure::SecondaryStructureRMSD, PLMD::adjmat::ClusterSize, PLMD::mapping::Mapping, PLMD::multicolvar::BridgedMultiColvarFunction, PLMD::adjmat::ClusterAnalysisBase, PLMD::gridtools::ActionWithGrid, PLMD::adjmat::ClusteringBase, and PLMD::gridtools::ActionWithIntegral.

turnOnHessian()

void PLMD::ves::Optimizer::turnOnHessian ( )

protectedinherited

unlockRequests()

virtual void PLMD::Action::unlockRequests ( )

inlinevirtualinherited

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

update()

void PLMD::ves::Optimizer::update ( )

virtualinherited

Update.

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

Reimplemented from PLMD::Action.

useCustomisableComponents()

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

staticinherited

The components in the action will depend on the user.

useDynamicStepSizeKeywords()

void PLMD::ves::Optimizer::useDynamicStepSizeKeywords ( Keywords &  keys )

staticinherited

useDynamicTargetDistributionKeywords()

void PLMD::ves::Optimizer::useDynamicTargetDistributionKeywords ( Keywords &  keys )

staticinherited

useFixedStepSizeKeywords()

void PLMD::ves::Optimizer::useFixedStepSizeKeywords ( Keywords &  keys )

staticinherited

useHessian()

bool PLMD::ves::Optimizer::useHessian ( ) const

inlineinherited

useHessianKeywords()

void PLMD::ves::Optimizer::useHessianKeywords ( Keywords &  keys )

staticinherited

useMaskKeywords()

void PLMD::ves::Optimizer::useMaskKeywords ( Keywords &  keys )

staticinherited

useMonitorAverageGradientKeywords()

void PLMD::ves::Optimizer::useMonitorAverageGradientKeywords ( Keywords &  keys )

staticinherited

useMultipleWalkers()

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

inlineinherited

useMultipleWalkersKeywords()

void PLMD::ves::Optimizer::useMultipleWalkersKeywords ( Keywords &  keys )

staticinherited

useNumericalDerivatives()

void PLMD::ActionWithValue::useNumericalDerivatives ( )

inlineinherited

This forces the class to use numerical derivatives.

useRestartKeywords()

void PLMD::ves::Optimizer::useRestartKeywords ( Keywords &  keys )

staticinherited

useReweightFactorKeywords()

void PLMD::ves::Optimizer::useReweightFactorKeywords ( Keywords &  keys )

staticinherited

warning()

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

inherited

Issue a warning.

writeBiasOutputFiles()

void PLMD::ves::Optimizer::writeBiasOutputFiles ( ) const

inherited

writeFesOutputFiles()

void PLMD::ves::Optimizer::writeFesOutputFiles ( ) const

inherited

writeFesProjOutputFiles()

void PLMD::ves::Optimizer::writeFesProjOutputFiles ( ) const

inherited

writeTargetDistOutputFiles()

void PLMD::ves::Optimizer::writeTargetDistOutputFiles ( ) const

inherited

writeTargetDistProjOutputFiles()

void PLMD::ves::Optimizer::writeTargetDistProjOutputFiles ( ) const

inherited

Member Data Documentation

comm

Communicator& PLMD::Action::comm

inherited

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.

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

• ves/Opt_Dummy.cpp