PLMD::generic::EffectiveEnergyDrift Class Reference

Provides the keyword EFFECTIVE_ENERGY_DRIFT More...

Inheritance diagram for PLMD::generic::EffectiveEnergyDrift:

Public Types
typedef std::vector< Action * >	Dependencies
typedef std::set< FILE * >::iterator	files_iterator

Public Member Functions
	EffectiveEnergyDrift (const ActionOptions &)
	~EffectiveEnergyDrift ()
void	calculate ()
	Calculate an Action. More...
void	apply ()
	Apply an Action. More...
void	update ()
	Update. More...
bool	onStep () const
	Check if the action is active on this step. 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...
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	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...
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...

Static Public Member Functions
static void	registerKeywords (Keywords &keys)

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
int	getStride () const

Private Attributes
OFile	output
long int	printStride
double	eed
Atoms &	atoms
vector< ActionWithValue * >	biases
long int	pDdStep
int	nLocalAtoms
int	pNLocalAtoms
vector< int >	pGatindex
vector< Vector >	positions
vector< Vector >	pPositions
vector< Vector >	forces
vector< Vector >	pForces
Tensor	box
Tensor	pbox
Tensor	fbox
Tensor	pfbox
const int	nProc
vector< int >	indexCnt
vector< int >	indexDsp
vector< int >	dataCnt
vector< int >	dataDsp
vector< int >	indexS
vector< int >	indexR
vector< double >	dataS
vector< double >	dataR
vector< int >	backmap
double	initialBias
bool	isFirstStep

Detailed Description

Provides the keyword EFFECTIVE_ENERGY_DRIFT

Member Typedef Documentation

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

inherited

typedef std::set<FILE*>::iterator PLMD::Action::files_iterator

inherited

Constructor & Destructor Documentation

PLMD::generic::EffectiveEnergyDrift::EffectiveEnergyDrift ( const ActionOptions &  ao )

explicit

PLMD::generic::EffectiveEnergyDrift::~EffectiveEnergyDrift

(

)

Member Function Documentation

void PLMD::Action::activate ( )

virtualinherited

Set action to active.

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

inherited

Specify that this Action depends on another one.

void PLMD::generic::EffectiveEnergyDrift::apply ( )

inlinevirtual

Apply an Action.

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

Implements PLMD::Action.

void PLMD::generic::EffectiveEnergyDrift::calculate ( )

inlinevirtual

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.

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

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::mapping::PCAVars, PLMD::ActionAtomistic, PLMD::analysis::Analysis, PLMD::multicolvar::MultiColvarFunction, PLMD::ActionWithArguments, PLMD::multicolvar::MultiColvarDensity, PLMD::multicolvar::BridgedMultiColvarFunction, PLMD::mapping::Mapping, and PLMD::vesselbase::ActionWithInputVessel.

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

inlinevirtualinherited

Check if the action needs gradient.

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

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

inlinevirtualinherited

Check if numerical derivatives should be performed.

Reimplemented in PLMD::ActionWithValue.

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

bool PLMD::Action::checkUpdate ( ) const

inherited

Check if action should be updated.

std::string PLMD::Action::cite ( const std::string &  s )

inherited

Cite a paper see PlumedMain::cite.

void PLMD::Action::clearDependencies ( )

inherited

Clear the dependence list for this Action.

void PLMD::Action::clearOptions ( )

virtualinherited

void PLMD::Action::deactivate ( )

inlinevirtualinherited

Set action to inactive.

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

inherited

Crash calculation and print documentation.

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

inherited

Exit with error code c.

int PLMD::Action::fclose ( FILE *  fp )

inherited

Closes a file opened with Action::fclose().

void PLMD::Action::fflush ( )

inherited

Tell to the Action to flush open files.

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)

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

inlineinherited

Return dependencies.

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

virtualinherited

bool PLMD::Action::getExchangeStep ( ) const

inherited

Check if we are on an exchange step.

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

inlineinherited

Returns the label.

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

inlineinherited

Returns the name.

bool PLMD::Action::getRestart ( ) const

inlineinherited

Return true if we are doing a restart.

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

inherited

Return the present timestep.

int PLMD::ActionPilot::getStride ( ) const

protectedinherited

double PLMD::Action::getTime ( ) const

inherited

Return the present time.

double PLMD::Action::getTimeStep ( ) const

inherited

Return the timestep.

bool PLMD::Action::isActive ( ) const

inlineinherited

Check if action is active.

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

inlineinherited

Check if an option is on.

virtual void PLMD::Action::lockRequests ( )

inlinevirtualinherited

Reimplemented in PLMD::mapping::PCAVars, PLMD::ActionAtomistic, PLMD::analysis::Analysis, PLMD::ActionWithArguments, and PLMD::mapping::Mapping.

bool PLMD::ActionPilot::onStep ( ) const

inherited

Check if the action is active on this step.

template<class T >

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

inherited

Parse one keyword as generic type.

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

inherited

Parse one keyword as boolean flag.

template<class T >

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

inherited

Parse one numbered keyword as generic type.

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.

template<class T >

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

inherited

Parse one keyword as std::vector.

void PLMD::Action::prepare ( )

virtualinherited

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

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

Reimplemented in PLMD::function::FuncPathMSD, PLMD::analysis::Analysis, PLMD::mapping::Mapping, PLMD::secondarystructure::SecondaryStructureRMSD, PLMD::generic::Read, PLMD::generic::Print, PLMD::colvar::Energy, and PLMD::colvar::CoordinationBase.

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.

void PLMD::generic::EffectiveEnergyDrift::registerKeywords ( Keywords &  keys )

static

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.

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

virtualinherited

virtual void PLMD::Action::unlockRequests ( )

inlinevirtualinherited

Reimplemented in PLMD::mapping::PCAVars, PLMD::ActionAtomistic, PLMD::analysis::Analysis, PLMD::ActionWithArguments, and PLMD::mapping::Mapping.

void PLMD::generic::EffectiveEnergyDrift::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.

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

inherited

Issue a warning.

Member Data Documentation

Atoms& PLMD::generic::EffectiveEnergyDrift::atoms

private

vector<int> PLMD::generic::EffectiveEnergyDrift::backmap

private

vector<ActionWithValue*> PLMD::generic::EffectiveEnergyDrift::biases

private

Tensor PLMD::generic::EffectiveEnergyDrift::box

private

Communicator& PLMD::Action::comm

inherited

vector<int> PLMD::generic::EffectiveEnergyDrift::dataCnt

private

vector<int> PLMD::generic::EffectiveEnergyDrift::dataDsp

private

vector<double> PLMD::generic::EffectiveEnergyDrift::dataR

private

vector<double> PLMD::generic::EffectiveEnergyDrift::dataS

private

double PLMD::generic::EffectiveEnergyDrift::eed

private

Tensor PLMD::generic::EffectiveEnergyDrift::fbox

private

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

inherited

vector<Vector> PLMD::generic::EffectiveEnergyDrift::forces

private

vector<int> PLMD::generic::EffectiveEnergyDrift::indexCnt

private

vector<int> PLMD::generic::EffectiveEnergyDrift::indexDsp

private

vector<int> PLMD::generic::EffectiveEnergyDrift::indexR

private

vector<int> PLMD::generic::EffectiveEnergyDrift::indexS

private

double PLMD::generic::EffectiveEnergyDrift::initialBias

private

bool PLMD::generic::EffectiveEnergyDrift::isFirstStep

private

const Keywords& PLMD::Action::keywords

inherited

Log& PLMD::Action::log

inherited

Reference to the log stream.

Communicator& PLMD::Action::multi_sim_comm

inherited

int PLMD::generic::EffectiveEnergyDrift::nLocalAtoms

private

const int PLMD::generic::EffectiveEnergyDrift::nProc

private

OFile PLMD::generic::EffectiveEnergyDrift::output

private

Tensor PLMD::generic::EffectiveEnergyDrift::pbox

private

long int PLMD::generic::EffectiveEnergyDrift::pDdStep

private

Tensor PLMD::generic::EffectiveEnergyDrift::pfbox

private

vector<Vector> PLMD::generic::EffectiveEnergyDrift::pForces

private

vector<int> PLMD::generic::EffectiveEnergyDrift::pGatindex

private

PlumedMain& PLMD::Action::plumed

inherited

Reference to main plumed object.

int PLMD::generic::EffectiveEnergyDrift::pNLocalAtoms

private

vector<Vector> PLMD::generic::EffectiveEnergyDrift::positions

private

vector<Vector> PLMD::generic::EffectiveEnergyDrift::pPositions

private

long int PLMD::generic::EffectiveEnergyDrift::printStride

private

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

• generic/EffectiveEnergyDrift.cpp