Main plumed object. More...

#include <PlumedMain.h>

Inheritance diagram for PLMD::PlumedMain:

Public Member Functions
std::string	cite (const std::string &)
	Add a citation, returning a string containing the reference number, something like "[10]". More...

unsigned	getNumThreads () const
	Get number of threads that can be used by openmp. More...

template<typename T >
unsigned	getGoodNumThreads (const T *x, unsigned s) const
	Get a reasonable number of threads so as to access to an array of size s located at x. More...

template<typename T >
unsigned	getGoodNumThreads (const std::vector< T > &v) const
	Get a reasonable number of threads so as to access to vector v;. More...

	PlumedMain ()

void	cmd (const std::string &key, void *val=NULL)
	cmd method, accessible with standard Plumed.h interface. More...

	~PlumedMain ()

void	readInputFile (std::string str)
	Read an input file. More...

void	readInputWords (const std::vector< std::string > &str)
	Read an input string. More...

void	readInputLine (const std::string &str)
	Read an input string. More...

void	init ()
	Initialize the object. More...

void	prepareCalc ()
	Prepare the calculation. More...

void	prepareDependencies ()
	Prepare the list of active Actions and needed atoms. More...

void	shareData ()
	Share the needed atoms. More...

void	performCalc ()
	Perform the calculation. More...

void	performCalcNoUpdate ()
	Perform the calculation without update() Shortcut for: waitData() + justCalculate() + backwardPropagate() More...

void	calc ()
	Complete PLUMED calculation. More...

void	waitData ()
	Scatters the needed atoms. More...

void	justCalculate ()
	Perform the forward loop on active actions. More...

void	justApply ()
	Backward propagate and update. More...

void	backwardPropagate ()
	Perform the backward loop on active actions. More...

void	update ()
	Call the update() method. More...

void	runJobsAtEndOfCalculation ()
	If there are calculations that need to be done at the very end of the calculations this makes sures they are done. More...

Atoms &	getAtoms ()
	Reference to atoms object. More...

const ActionSet &	getActionSet () const
	Reference to the list of Action's. More...

Log &	getLog ()
	Referenge to the log stream. More...

long int	getStep () const
	Return the number of the step. More...

void	exit (int c=0)
	Stop the run. More...

void	load (const std::string &)
	Load a shared library. More...

const std::string &	getSuffix () const
	Get the suffix string. More...

void	setSuffix (const std::string &)
	Set the suffix string. More...

double	getBias () const
	get the value of the bias More...

double	getWork () const
	get the value of the work More...

FILE *	fopen (const char path, const char mode)
	Opens a file. More...

int	fclose (FILE *fp)
	Closes a file opened with PlumedMain::fopen() More...

void	insertFile (FileBase &)
	Insert a file. More...

void	eraseFile (FileBase &)
	Erase a file. More...

void	fflush ()
	Flush all files. More...

bool	getRestart () const
	Check if restarting. More...

void	setRestart (bool f)
	Set restart flag. More...

bool	getCPT () const
	Check if checkpointing. More...

void	setExchangeStep (bool f)
	Set exchangeStep flag. More...

bool	getExchangeStep () const
	Get exchangeStep flag. More...

void	stop ()
	Stop the calculation cleanly (both the MD code and plumed) More...

void	resetActive (bool active)
	Enforce active flag. More...

ExchangePatterns &	getExchangePatterns ()
	Access to exchange patterns. More...

void	updateFlagsPush (bool)
	Push a state to update flags. More...

void	updateFlagsPop ()
	Pop a state from update flags. More...

bool	updateFlagsTop ()
	Get top of update flags. More...

void	setEndPlumed ()
	Set end of input file. More...

void	cmd (const std::string &key, const void *val)
	Const val version, which indeed just overrides the const and call the virtual method. More...

virtual void	cmd (const std::string &key, void *val=NULL)=0
	This has to be implemented in daughter classes. More...

void	cmd (const std::string &key, const void *val)
	Const val version, which indeed just overrides the const and call the virtual method. More...

Public Attributes
Communicator &	comm
	Communicator for plumed. More...

Communicator &	multi_sim_comm

bool	novirial
	Flag to switch off virial calculation (for debug and MD codes with no barostat) More...

bool	detailedTimers
	Flag to switch on detailed timers. More...

std::map< std::string, double >	passMap
	Generic map string -> double intended to pass information across Actions. More...

Private Attributes
DLLoader &	dlloader

WithCmd *	cltool

Stopwatch &	stopwatch

WithCmd *	grex

bool	initialized
	Flag to avoid double initialization. More...

std::string	MDEngine
	Name of MD engine. More...

Log &	log
	Log stream. More...

Citations &	citations
	tools/Citations.holder More...

long int	step
	Present step number. More...

bool	active
	Condition for plumed to be active. More...

std::string	plumedDat
	Name of the input file. More...

bool	endPlumed
	End of input file. More...

Atoms &	atoms
	Object containing information about atoms (such as positions,...). More...

ActionSet &	actionSet
	Set of actions found in plumed.dat file. More...

std::vector< ActionPilot * >	pilots
	Set of Pilot actions. More...

std::string	suffix
	Suffix string for file opening, useful for multiple simulations in the same directory. More...

double	bias
	The total bias (=total energy of the restraints) More...

double	work
	The total work. More...

ExchangePatterns &	exchangePatterns
	Class of possible exchange patterns, used for BIASEXCHANGE but also for future parallel tempering. More...

bool	exchangeStep
	Set to true if on an exchange step. More...

bool	restart
	Flag for restart. More...

bool	doCheckPoint
	Flag for checkpointig. More...

std::set< FileBase * >	files

int *	stopFlag
	Stuff to make plumed stop the MD code cleanly. More...

bool	stopNow

std::stack< bool >	updateFlags
	Stack for update flags. More...

Detailed Description

Main plumed object.

In MD engines this object is not manipulated directly but it is wrapped in plumed or PLMD::Plumed objects. Its main method is cmd(), which defines completely the external plumed interface. It does not contain any static data.

Constructor & Destructor Documentation

◆ PlumedMain()

PLMD::PlumedMain::PlumedMain ( )

◆ ~PlumedMain()

PLMD::PlumedMain::~PlumedMain ( )

Member Function Documentation

◆ backwardPropagate()

void PLMD::PlumedMain::backwardPropagate ( )

Perform the backward loop on active actions.

Needed to apply the forces back.

◆ calc()

void PLMD::PlumedMain::calc ( )

Complete PLUMED calculation.

Shortcut for prepareCalc() + performCalc()

◆ cite()

std::string PLMD::PlumedMain::cite ( const std::string & item )

Add a citation, returning a string containing the reference number, something like "[10]".

◆ cmd() [1/4]

void PLMD::WithCmd::cmd	(	const std::string &	key,
		const void *	val
	)

inlineinherited

Const val version, which indeed just overrides the const and call the virtual method.

◆ cmd() [2/4]

void PLMD::WithCmd::cmd

inline

Const val version, which indeed just overrides the const and call the virtual method.

◆ cmd() [3/4]

virtual void PLMD::WithCmd::cmd

This has to be implemented in daughter classes.

◆ cmd() [4/4]

void PLMD::PlumedMain::cmd	(	const std::string &	key,
		void *	val = `NULL`
	)

virtual

cmd method, accessible with standard Plumed.h interface.

Parameters

key	The name of the command to be executed.
val	The argument of the command to be executed. It is called as plumed_cmd() or as PLMD::Plumed::cmd() It is the interpreter for plumed commands. It basically contains the definition of the plumed interface. If you want to add a new functionality to the interface between plumed and an MD engine, this is the right place Notice that this interface should always keep retro-compatibility

Implements PLMD::WithCmd.

◆ eraseFile()

void PLMD::PlumedMain::eraseFile ( FileBase & f )

Erase a file.

◆ exit()

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

Stop the run.

◆ fclose()

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

Closes a file opened with PlumedMain::fopen()

◆ fflush()

void PLMD::PlumedMain::fflush ( )

Flush all files.

◆ fopen()

FILE * PLMD::PlumedMain::fopen	(	const char *	path,
		const char *	mode
	)

Opens a file.

Similar to plain fopen, but, if it finds an error in opening the file, it also tries with path+suffix. This trick is useful for multiple replica simulations.

◆ getActionSet()

const ActionSet & PLMD::PlumedMain::getActionSet ( ) const

inline

Reference to the list of Action's.

◆ getAtoms()

Atoms & PLMD::PlumedMain::getAtoms ( )

inline

Reference to atoms object.

◆ getBias()

double PLMD::PlumedMain::getBias ( ) const

get the value of the bias

◆ getCPT()

bool PLMD::PlumedMain::getCPT ( ) const

inline

Check if checkpointing.

◆ getExchangePatterns()

ExchangePatterns& PLMD::PlumedMain::getExchangePatterns ( )

inline

Access to exchange patterns.

◆ getExchangeStep()

bool PLMD::PlumedMain::getExchangeStep ( ) const

inline

Get exchangeStep flag.

◆ getGoodNumThreads() [1/2]

template<typename T >

unsigned PLMD::PlumedMain::getGoodNumThreads	(	const T *	x,
		unsigned	s
	)		const

Get a reasonable number of threads so as to access to an array of size s located at x.

◆ getGoodNumThreads() [2/2]

template<typename T >

unsigned PLMD::PlumedMain::getGoodNumThreads ( const std::vector< T > & v ) const

Get a reasonable number of threads so as to access to vector v;.

◆ getLog()

Log & PLMD::PlumedMain::getLog ( )

Referenge to the log stream.

◆ getNumThreads()

unsigned PLMD::PlumedMain::getNumThreads ( ) const

Get number of threads that can be used by openmp.

◆ getRestart()

bool PLMD::PlumedMain::getRestart ( ) const

inline

Check if restarting.

◆ getStep()

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

inline

Return the number of the step.

◆ getSuffix()

const std::string & PLMD::PlumedMain::getSuffix ( ) const

inline

Get the suffix string.

◆ getWork()

double PLMD::PlumedMain::getWork ( ) const

get the value of the work

◆ init()

void PLMD::PlumedMain::init ( )

Initialize the object.

Should be called once.

◆ insertFile()

void PLMD::PlumedMain::insertFile ( FileBase & f )

Insert a file.

◆ justApply()

void PLMD::PlumedMain::justApply ( )

Backward propagate and update.

Shortcut for backwardPropagate() + update() I leave it here for backward compatibility

◆ justCalculate()

void PLMD::PlumedMain::justCalculate ( )

Perform the forward loop on active actions.

◆ load()

void PLMD::PlumedMain::load ( const std::string & ss )

Load a shared library.

◆ performCalc()

void PLMD::PlumedMain::performCalc ( )

Perform the calculation.

Shortcut for waitData() + justCalculate() + justApply(). Equivalently: waitData() + justCalculate() + backwardPropagate() + update().

◆ performCalcNoUpdate()

void PLMD::PlumedMain::performCalcNoUpdate ( )

Perform the calculation without update() Shortcut for: waitData() + justCalculate() + backwardPropagate()

◆ prepareCalc()

void PLMD::PlumedMain::prepareCalc ( )

Prepare the calculation.

Here it is checked which are the active Actions and communication of the relevant atoms is initiated. Shortcut for prepareDependencies() + shareData()

◆ prepareDependencies()

void PLMD::PlumedMain::prepareDependencies ( )

Prepare the list of active Actions and needed atoms.

Scan the Actions to see which are active and which are not, so as to prepare a list of the atoms needed at this step.

◆ readInputFile()

void PLMD::PlumedMain::readInputFile ( std::string str )

Read an input file.

Parameters

str	name of the file

◆ readInputLine()

void PLMD::PlumedMain::readInputLine ( const std::string & str )

Read an input string.

Parameters

str	name of the string At variance with readInputWords(), this is splitting the string into words

◆ readInputWords()

void PLMD::PlumedMain::readInputWords ( const std::vector< std::string > & str )

Read an input string.

Parameters

str	name of the string

◆ resetActive()

void PLMD::PlumedMain::resetActive ( bool active )

inline

Enforce active flag.

This is a (bit dirty) hack to solve a bug. When there is no active ActionPilot, several shortcuts are used. However, these shortcuts can block GREX module. This function allows to enforce active plumed when doing exchanges, thus fixing the bug.

◆ runJobsAtEndOfCalculation()

void PLMD::PlumedMain::runJobsAtEndOfCalculation ( )

If there are calculations that need to be done at the very end of the calculations this makes sures they are done.

◆ setEndPlumed()

void PLMD::PlumedMain::setEndPlumed ( )

inline

Set end of input file.

◆ setExchangeStep()

void PLMD::PlumedMain::setExchangeStep ( bool f )

inline

Set exchangeStep flag.

◆ setRestart()

void PLMD::PlumedMain::setRestart ( bool f )

inline

Set restart flag.

◆ setSuffix()

void PLMD::PlumedMain::setSuffix ( const std::string & s )

inline

Set the suffix string.

◆ shareData()

void PLMD::PlumedMain::shareData ( )

Share the needed atoms.

In asynchronous implementations, this method sends the required atoms to all the plumed processes, without waiting for the communication to complete.

◆ stop()

void PLMD::PlumedMain::stop ( )

Stop the calculation cleanly (both the MD code and plumed)

◆ update()

void PLMD::PlumedMain::update ( )

Call the update() method.

◆ updateFlagsPop()

void PLMD::PlumedMain::updateFlagsPop ( )

inline

Pop a state from update flags.

◆ updateFlagsPush()

void PLMD::PlumedMain::updateFlagsPush ( bool on )

inline

Push a state to update flags.

◆ updateFlagsTop()

bool PLMD::PlumedMain::updateFlagsTop ( )

inline

Get top of update flags.

◆ waitData()

void PLMD::PlumedMain::waitData ( )

Scatters the needed atoms.

In asynchronous implementations, this method waits for the communications started in shareData() to be completed. Otherwise, just send around needed atoms.

Member Data Documentation

◆ actionSet

ActionSet& PLMD::PlumedMain::actionSet

private

Set of actions found in plumed.dat file.

◆ active

bool PLMD::PlumedMain::active

private

Condition for plumed to be active.

At every step, PlumedMain is checking if there are Action's requiring some work. If at least one Action requires some work, this variable is set to true.

◆ atoms

Atoms& PLMD::PlumedMain::atoms

private

Object containing information about atoms (such as positions,...).

◆ bias

double PLMD::PlumedMain::bias

private

The total bias (=total energy of the restraints)

◆ citations

Citations& PLMD::PlumedMain::citations

private

tools/Citations.holder

◆ cltool

WithCmd* PLMD::PlumedMain::cltool

private

◆ comm

Communicator& PLMD::PlumedMain::comm

Communicator for plumed.

Includes all the processors used by plumed.

◆ detailedTimers

bool PLMD::PlumedMain::detailedTimers

Flag to switch on detailed timers.

◆ dlloader

DLLoader& PLMD::PlumedMain::dlloader

private

◆ doCheckPoint

bool PLMD::PlumedMain::doCheckPoint

private

Flag for checkpointig.

◆ endPlumed

bool PLMD::PlumedMain::endPlumed

private

End of input file.

Set to true to terminate reading

◆ exchangePatterns

ExchangePatterns& PLMD::PlumedMain::exchangePatterns

private

Class of possible exchange patterns, used for BIASEXCHANGE but also for future parallel tempering.

◆ exchangeStep

bool PLMD::PlumedMain::exchangeStep

private

Set to true if on an exchange step.

◆ files

std::set<FileBase*> PLMD::PlumedMain::files

private

◆ grex

WithCmd* PLMD::PlumedMain::grex

private

◆ initialized

bool PLMD::PlumedMain::initialized

private

Flag to avoid double initialization.

◆ log

Log& PLMD::PlumedMain::log

private

Log stream.

◆ MDEngine

std::string PLMD::PlumedMain::MDEngine

private

Name of MD engine.

◆ multi_sim_comm

Communicator& PLMD::PlumedMain::multi_sim_comm

◆ novirial

bool PLMD::PlumedMain::novirial

Flag to switch off virial calculation (for debug and MD codes with no barostat)

◆ passMap

std::map<std::string,double> PLMD::PlumedMain::passMap

Generic map string -> double intended to pass information across Actions.

◆ pilots

std::vector<ActionPilot*> PLMD::PlumedMain::pilots

private

Set of Pilot actions.

These are the action the, if they are Pilot::onStep(), can trigger execution

◆ plumedDat

std::string PLMD::PlumedMain::plumedDat

private

Name of the input file.

◆ restart

bool PLMD::PlumedMain::restart

private

Flag for restart.

◆ step

long int PLMD::PlumedMain::step

private

Present step number.

◆ stopFlag

int* PLMD::PlumedMain::stopFlag

private

Stuff to make plumed stop the MD code cleanly.

◆ stopNow

bool PLMD::PlumedMain::stopNow

private

◆ stopwatch

Stopwatch& PLMD::PlumedMain::stopwatch

private

◆ suffix

std::string PLMD::PlumedMain::suffix

private

Suffix string for file opening, useful for multiple simulations in the same directory.

◆ updateFlags

std::stack<bool> PLMD::PlumedMain::updateFlags

private

Stack for update flags.

Store information used in class generic::UpdateIf

◆ work

double PLMD::PlumedMain::work

private

The total work.

This computed by accumulating the change in external potentials.

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

core/PlumedMain.h
core/PlumedMain.cpp

Public Member Functions

Public Attributes

Private Attributes

Detailed Description

Constructor & Destructor Documentation

◆ PlumedMain()

◆ ~PlumedMain()

Member Function Documentation

◆ backwardPropagate()

◆ calc()

◆ cite()

◆ cmd() [1/4]

◆ cmd() [2/4]

◆ cmd() [3/4]

◆ cmd() [4/4]

◆ eraseFile()

◆ exit()

◆ fclose()

◆ fflush()

◆ fopen()

◆ getActionSet()

◆ getAtoms()

◆ getBias()

◆ getCPT()

◆ getExchangePatterns()

◆ getExchangeStep()

◆ getGoodNumThreads() [1/2]

◆ getGoodNumThreads() [2/2]

◆ getLog()

◆ getNumThreads()

◆ getRestart()

◆ getStep()

◆ getSuffix()

◆ getWork()

◆ init()

◆ insertFile()

◆ justApply()

◆ justCalculate()

◆ load()

◆ performCalc()

◆ performCalcNoUpdate()

◆ prepareCalc()

◆ prepareDependencies()

◆ readInputFile()

◆ readInputLine()

◆ readInputWords()

◆ resetActive()

◆ runJobsAtEndOfCalculation()

◆ setEndPlumed()

◆ setExchangeStep()

◆ setRestart()

◆ setSuffix()

◆ shareData()

◆ stop()

◆ update()

◆ updateFlagsPop()

◆ updateFlagsPush()

◆ updateFlagsTop()

◆ waitData()

Member Data Documentation

◆ actionSet

◆ active

◆ atoms

◆ bias

◆ citations

◆ cltool

◆ comm

◆ detailedTimers

◆ dlloader

◆ doCheckPoint

◆ endPlumed

◆ exchangePatterns

◆ exchangeStep

◆ files

◆ grex

◆ initialized

◆ log

◆ MDEngine

◆ multi_sim_comm

◆ novirial