PLMD::bias::MetaD Class Reference

Provides the keyword METAD More...

Inheritance diagram for PLMD::bias::MetaD:

Classes
struct	Gaussian
struct	TemperingSpecs

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

Public Member Functions
	MetaD (const ActionOptions &)
	~MetaD ()
void	calculate ()
	Calculate an Action. More...
void	update ()
	Update. More...
bool	checkNeedsGradients () const
	Check if the action needs gradient. More...
void	apply ()
	Apply an Action. More...
unsigned	getNumberOfDerivatives ()
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 ()
void	lockRequests ()
virtual void	unlockRequests ()
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 void	calculateNumericalDerivatives (ActionWithValue *a=NULL)
	Perform calculation using numerical derivatives N.B. More...
virtual void	calculateNumericalDerivatives (ActionWithValue *a=NULL)
	Calculate the 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...
double	getProjection (unsigned i, unsigned j) const
	Get the scalar product between the gradients of two variables. More...
double	getArgument (const unsigned n) const
	Returns the value of an argument. More...
Value *	getPntrToArgument (const unsigned n)
	Return a pointer to specific argument. More...
virtual unsigned	getNumberOfArguments () const
	Returns the number of arguments. More...
double	difference (int, double, double) const
	Takes the difference taking into account pbc for arg i. More...
double	bringBackInPbc (int i, double d1) const
	Takes one value and brings it back into the pbc of argument i. More...
void	parseArgumentList (const std::string &key, std::vector< Value *> &args)
	Parse a list of arguments. More...
bool	parseArgumentList (const std::string &key, int i, std::vector< Value *> &args)
	Parse a numbered list of arguments. More...
void	requestArguments (const std::vector< Value *> &arg)
	Setup the dependencies. More...
void	addForcesOnArguments (const std::vector< double > &forces)
	Add forces to arguments (used in apply) More...
const std::vector< Value * > &	getArguments () const
	Returns an array of pointers to the arguments. More...
void	interpretArgumentList (const std::vector< std::string > &c, std::vector< Value *> &arg)
	Convert a list of argument names into a list of pointers to the values. More...

Static Public Member Functions
static void	registerKeywords (Keywords &keys)
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	setOutputForce (int i, double f)
	set the force from the bias on argument i, this automatically set the partial derivative of the bias with respect to i to -f More...
void	setBias (double bias)
	set the value of the bias More...
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...
void	expandArgKeywordInPDB (PDB &pdb)
	This changes the arg keyword in the pdb file. More...

Private Member Functions
void	readTemperingSpecs (TemperingSpecs &t_specs)
void	logTemperingSpecs (const TemperingSpecs &t_specs)
void	readGaussians (IFile *)
bool	readChunkOfGaussians (IFile *ifile, unsigned n)
void	writeGaussian (const Gaussian &, OFile &)
void	addGaussian (const Gaussian &)
double	getHeight (const vector< double > &)
void	temperHeight (double &height, const TemperingSpecs &t_specs, const double tempering_bias)
double	getBiasAndDerivatives (const vector< double > &, double *der=NULL)
double	evaluateGaussian (const vector< double > &, const Gaussian &, double *der=NULL)
double	getGaussianNormalization (const Gaussian &)
vector< unsigned >	getGaussianSupport (const Gaussian &)
bool	scanOneHill (IFile *ifile, vector< Value > &v, vector< double > &center, vector< double > &sigma, double &height, bool &multivariate)
	takes a pointer to the file and a template string with values v and gives back the next center, sigma and height More...
void	computeReweightingFactor ()
double	getTransitionBarrierBias ()

Static Private Member Functions
static void	registerTemperingKeywords (const std::string &name_stem, const std::string &name, Keywords &keys)

Private Attributes
vector< double >	sigma0_
vector< double >	sigma0min_
vector< double >	sigma0max_
vector< Gaussian >	hills_
OFile	hillsOfile_
OFile	gridfile_
Grid *	BiasGrid_
bool	storeOldGrids_
int	wgridstride_
bool	grid_
double	height0_
double	biasf_
double	dampfactor_
struct TemperingSpecs	tt_specs_
std::string	targetfilename_
Grid *	TargetGrid_
double	kbt_
int	stride_
bool	welltemp_
double *	dp_
int	adaptive_
FlexibleBin *	flexbin
int	mw_n_
string	mw_dir_
int	mw_id_
int	mw_rstride_
bool	walkers_mpi
unsigned	mpi_nw_
unsigned	mpi_mw_
bool	acceleration
double	acc
double	acc_restart_mean_
bool	calc_max_bias_
double	max_bias_
bool	calc_transition_bias_
double	transition_bias_
vector< vector< double > >	transitionwells_
vector< IFile * >	ifiles
vector< string >	ifilesnames
double	uppI_
double	lowI_
bool	doInt_
bool	isFirstStep
double	reweight_factor
vector< unsigned >	rewf_grid_
unsigned	rewf_ustride_
double	work_
long int	last_step_warn_grid
string	fmt

Static Private Attributes
static const size_t	n_tempering_options_ = 1
static const string	tempering_names_ [1][2] = {{"TT", "transition tempered"}}

Detailed Description

Provides the keyword METAD

Member Typedef Documentation

Dependencies

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

inherited

Constructor & Destructor Documentation

MetaD()

PLMD::bias::MetaD::MetaD ( const ActionOptions &  ao )

explicit

~MetaD()

PLMD::bias::MetaD::~MetaD

(

)

Member Function Documentation

activate()

void PLMD::Action::activate ( )

virtualinherited

Set action to active.

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.

addForcesOnArguments()

void PLMD::ActionWithArguments::addForcesOnArguments ( const std::vector< double > &  forces )

inherited

Add forces to arguments (used in apply)

addGaussian()

void PLMD::bias::MetaD::addGaussian ( const Gaussian &  hill )

private

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::bias::Bias::apply ( )

virtualinherited

Apply an Action.

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

Implements PLMD::Action.

Reimplemented in PLMD::ves::VesBias.

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.

bringBackInPbc()

double PLMD::ActionWithArguments::bringBackInPbc ( int  i, double  d1  ) const

inlineinherited

Takes one value and brings it back into the pbc of argument i.

calculate()

void PLMD::bias::MetaD::calculate ( )

virtual

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() [1/2]

void PLMD::ActionWithArguments::calculateNumericalDerivatives ( ActionWithValue *  a = NULL )

virtualinherited

Calculate the numerical derivatives N.B.

only pass an ActionWithValue to this routine if you know exactly what you are doing. The default will be correct for the vast majority of cases

Reimplemented from PLMD::Action.

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

calculateNumericalDerivatives() [2/2]

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()

bool PLMD::bias::MetaD::checkNeedsGradients ( ) const

virtual

Check if the action needs gradient.

Reimplemented from PLMD::Action.

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

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.

computeReweightingFactor()

void PLMD::bias::MetaD::computeReweightingFactor ( )

private

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.

difference()

double PLMD::ActionWithArguments::difference ( int  i, double  d1, double  d2  ) const

inlineinherited

Takes the difference taking into account pbc for arg i.

doNotCalculateDerivatives()

bool PLMD::ActionWithValue::doNotCalculateDerivatives ( ) const

inlinevirtualinherited

Are we not calculating derivatives.

Reimplemented in PLMD::multicolvar::MultiColvarBase.

error()

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

inherited

Crash calculation and print documentation.

evaluateGaussian()

double PLMD::bias::MetaD::evaluateGaussian ( const vector< double > &  cv, const Gaussian &  hill, double *  der = NULL  )

private

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.

expandArgKeywordInPDB()

void PLMD::ActionWithArguments::expandArgKeywordInPDB ( PDB &  pdb )

protectedinherited

This changes the arg keyword in the pdb file.

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)

getArgument()

double PLMD::ActionWithArguments::getArgument ( const unsigned  n ) const

inlineinherited

Returns the value of an argument.

getArguments()

const std::vector< Value * > & PLMD::ActionWithArguments::getArguments ( ) const

inlineinherited

Returns an array of pointers to the arguments.

getBiasAndDerivatives()

double PLMD::bias::MetaD::getBiasAndDerivatives ( const vector< double > &  cv, double *  der = NULL  )

private

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.

getDependencies()

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

inlineinherited

Return dependencies.

getDocumentation()

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

virtualinherited

getExchangeStep()

bool PLMD::Action::getExchangeStep ( ) const

inherited

Check if we are on an exchange step.

getGaussianNormalization()

double PLMD::bias::MetaD::getGaussianNormalization ( const Gaussian &  hill )

private

getGaussianSupport()

vector< unsigned > PLMD::bias::MetaD::getGaussianSupport ( const Gaussian &  hill )

private

getHeight()

double PLMD::bias::MetaD::getHeight ( const vector< double > &  cv )

private

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.

getNumberOfArguments()

unsigned PLMD::ActionWithArguments::getNumberOfArguments ( ) const

inlinevirtualinherited

Returns the number of arguments.

Reimplemented in PLMD::vesselbase::ActionWithAveraging.

getNumberOfComponents()

int PLMD::ActionWithValue::getNumberOfComponents ( ) const

inlineinherited

Returns the number of values defined.

getNumberOfDerivatives()

unsigned PLMD::bias::Bias::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)

getPntrToArgument()

Value * PLMD::ActionWithArguments::getPntrToArgument ( const unsigned  n )

inlineinherited

Return a pointer to specific argument.

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.

getProjection()

double PLMD::ActionWithArguments::getProjection ( unsigned  i, unsigned  j  ) const

inherited

Get the scalar product between the gradients of two variables.

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.

getStride()

int PLMD::ActionPilot::getStride ( ) const

inherited

Get the stride.

getTime()

double PLMD::Action::getTime ( ) const

inherited

Return the present time.

getTimeStep()

double PLMD::Action::getTimeStep ( ) const

inherited

Return the timestep.

getTransitionBarrierBias()

double PLMD::bias::MetaD::getTransitionBarrierBias ( )

private

interpretArgumentList()

void PLMD::ActionWithArguments::interpretArgumentList ( const std::vector< std::string > &  c, std::vector< Value *> &  arg  )

inherited

Convert a list of argument names into a list of pointers to the values.

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.

lockRequests() [1/2]

void PLMD::ActionWithArguments::lockRequests ( )

inlinevirtualinherited

Reimplemented from PLMD::Action.

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

lockRequests() [2/2]

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.

logTemperingSpecs()

void PLMD::bias::MetaD::logTemperingSpecs ( const TemperingSpecs &  t_specs )

private

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.

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.

parseArgumentList() [1/2]

void PLMD::ActionWithArguments::parseArgumentList ( const std::string &  key, std::vector< Value *> &  args  )

inherited

Parse a list of arguments.

parseArgumentList() [2/2]

bool PLMD::ActionWithArguments::parseArgumentList ( const std::string &  key, int  i, std::vector< Value *> &  args  )

inherited

Parse a numbered list of arguments.

parseFlag()

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

inherited

Parse one keyword as boolean flag.

parseNumbered()

template<class T >

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

inherited

Parse one numbered keyword as generic type.

parseNumberedVector()

template<class T >

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

inherited

Parse a vector with a number.

parseVector()

template<class T >

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

inherited

Parse one keyword as std::vector.

prepare()

void PLMD::Action::prepare ( )

virtualinherited

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

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

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

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.

readChunkOfGaussians()

bool PLMD::bias::MetaD::readChunkOfGaussians ( IFile *  ifile, unsigned  n  )

private

readGaussians()

void PLMD::bias::MetaD::readGaussians ( IFile *  ifile )

private

readTemperingSpecs()

void PLMD::bias::MetaD::readTemperingSpecs ( TemperingSpecs &  t_specs )

private

registerKeywords()

void PLMD::bias::MetaD::registerKeywords ( Keywords &  keys )

static

registerTemperingKeywords()

void PLMD::bias::MetaD::registerTemperingKeywords ( const std::string &  name_stem, const std::string &  name, Keywords &  keys  )

staticprivate

requestArguments()

void PLMD::ActionWithArguments::requestArguments ( const std::vector< Value *> &  arg )

inherited

Setup the dependencies.

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.

scanOneHill()

bool PLMD::bias::MetaD::scanOneHill ( IFile *  ifile, vector< Value > &  v, vector< double > &  center, vector< double > &  sigma, double &  height, bool &  multivariate  )

private

takes a pointer to the file and a template string with values v and gives back the next center, sigma and height

setBias()

void PLMD::bias::Bias::setBias ( double  bias )

inlineprotectedinherited

set the value of the bias

setGradientsIfNeeded()

void PLMD::ActionWithValue::setGradientsIfNeeded ( )

inherited

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

setNotPeriodic()

void PLMD::ActionWithValue::setNotPeriodic ( )

inherited

Set your default value to have no periodicity.

setOption()

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

virtualinherited

setOutputForce()

void PLMD::bias::Bias::setOutputForce ( int  i, double  f  )

inlineprotectedinherited

set the force from the bias on argument i, this automatically set the partial derivative of the bias with respect to i to -f

setPeriodic()

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

inherited

Set the value to be periodic with a particular domain.

setStride()

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

inherited

Set the value of the stride.

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.

temperHeight()

void PLMD::bias::MetaD::temperHeight ( double &  height, const TemperingSpecs &  t_specs, const double  tempering_bias  )

private

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.

unlockRequests() [1/2]

void PLMD::ActionWithArguments::unlockRequests ( )

inlinevirtualinherited

Reimplemented from PLMD::Action.

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

unlockRequests() [2/2]

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::bias::MetaD::update ( )

virtual

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.

useNumericalDerivatives()

void PLMD::ActionWithValue::useNumericalDerivatives ( )

inlineinherited

This forces the class to use numerical derivatives.

warning()

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

inherited

Issue a warning.

writeGaussian()

void PLMD::bias::MetaD::writeGaussian ( const Gaussian &  hill, OFile &  file  )

private

Member Data Documentation

acc

double PLMD::bias::MetaD::acc

private

acc_restart_mean_

double PLMD::bias::MetaD::acc_restart_mean_

private

acceleration

bool PLMD::bias::MetaD::acceleration

private

adaptive_

int PLMD::bias::MetaD::adaptive_

private

biasf_

double PLMD::bias::MetaD::biasf_

private

BiasGrid_

Grid* PLMD::bias::MetaD::BiasGrid_

private

calc_max_bias_

bool PLMD::bias::MetaD::calc_max_bias_

private

calc_transition_bias_

bool PLMD::bias::MetaD::calc_transition_bias_

private

comm

Communicator& PLMD::Action::comm

inherited

dampfactor_

double PLMD::bias::MetaD::dampfactor_

private

doInt_

bool PLMD::bias::MetaD::doInt_

private

dp_

double* PLMD::bias::MetaD::dp_

private

files

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

inherited

flexbin

FlexibleBin* PLMD::bias::MetaD::flexbin

private

fmt

string PLMD::bias::MetaD::fmt

private

grid_

bool PLMD::bias::MetaD::grid_

private

gridfile_

OFile PLMD::bias::MetaD::gridfile_

private

height0_

double PLMD::bias::MetaD::height0_

private

hills_

vector<Gaussian> PLMD::bias::MetaD::hills_

private

hillsOfile_

OFile PLMD::bias::MetaD::hillsOfile_

private

ifiles

vector<IFile*> PLMD::bias::MetaD::ifiles

private

ifilesnames

vector<string> PLMD::bias::MetaD::ifilesnames

private

isFirstStep

bool PLMD::bias::MetaD::isFirstStep

private

kbt_

double PLMD::bias::MetaD::kbt_

private

keywords

const Keywords& PLMD::Action::keywords

inherited

last_step_warn_grid

long int PLMD::bias::MetaD::last_step_warn_grid

private

log

Log& PLMD::Action::log

inherited

Reference to the log stream.

lowI_

double PLMD::bias::MetaD::lowI_

private

max_bias_

double PLMD::bias::MetaD::max_bias_

private

mpi_mw_

unsigned PLMD::bias::MetaD::mpi_mw_

private

mpi_nw_

unsigned PLMD::bias::MetaD::mpi_nw_

private

multi_sim_comm

Communicator& PLMD::Action::multi_sim_comm

inherited

mw_dir_

string PLMD::bias::MetaD::mw_dir_

private

mw_id_

int PLMD::bias::MetaD::mw_id_

private

mw_n_

int PLMD::bias::MetaD::mw_n_

private

mw_rstride_

int PLMD::bias::MetaD::mw_rstride_

private

n_tempering_options_

const size_t PLMD::bias::MetaD::n_tempering_options_ = 1

staticprivate

plumed

PlumedMain& PLMD::Action::plumed

inherited

Reference to main plumed object.

reweight_factor

double PLMD::bias::MetaD::reweight_factor

private

rewf_grid_

vector<unsigned> PLMD::bias::MetaD::rewf_grid_

private

rewf_ustride_

unsigned PLMD::bias::MetaD::rewf_ustride_

private

sigma0_

vector<double> PLMD::bias::MetaD::sigma0_

private

sigma0max_

vector<double> PLMD::bias::MetaD::sigma0max_

private

sigma0min_

vector<double> PLMD::bias::MetaD::sigma0min_

private

storeOldGrids_

bool PLMD::bias::MetaD::storeOldGrids_

private

stride_

int PLMD::bias::MetaD::stride_

private

targetfilename_

std::string PLMD::bias::MetaD::targetfilename_

private

TargetGrid_

Grid* PLMD::bias::MetaD::TargetGrid_

private

tempering_names_

const std::string PLMD::bias::MetaD::tempering_names_ = {{"TT", "transition tempered"}}

staticprivate

transition_bias_

double PLMD::bias::MetaD::transition_bias_

private

transitionwells_

vector<vector<double> > PLMD::bias::MetaD::transitionwells_

private

tt_specs_

struct TemperingSpecs PLMD::bias::MetaD::tt_specs_

private

uppI_

double PLMD::bias::MetaD::uppI_

private

walkers_mpi

bool PLMD::bias::MetaD::walkers_mpi

private

welltemp_

bool PLMD::bias::MetaD::welltemp_

private

wgridstride_

int PLMD::bias::MetaD::wgridstride_

private

work_

double PLMD::bias::MetaD::work_

private

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

• bias/MetaD.cpp