Main plumed object. More...

#include <PlumedMain.h>

Inheritance diagram for PLMD::PlumedMain:

Classes
struct	plumed_error_handler
	Error handler. More...

Public Member Functions
	PlumedMain ()

	~PlumedMain ()

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

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

bool	callErrorHandler (int code, const char *msg) const
	Call error handler. More...

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

void	cmd (const std::string &key, const TypesafePtr &val, const std::size_t *shape)

void	cmd (const std::string &key, const TypesafePtr &val, const std::size_t *shape)

void	cmd (const std::string &key, const TypesafePtr &val, std::size_t nelem, const std::size_t *shape=nullptr)

void	cmd (const std::string &key, const TypesafePtr &val, std::size_t nelem, const std::size_t *shape=nullptr)

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

virtual void	cmd (const std::string &key, const TypesafePtr &val=nullptr)=0

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

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

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

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

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

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

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

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

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

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

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

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...

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

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

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

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

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

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

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

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

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

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

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

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

void	performCalcNoForces ()
	Perform the calculation without backpropagation nor update() Shortcut for: waitData() + justCalculate() More...

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

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

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

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

void	readInputFile (IFile &ifile)
	Read an input file. More...

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

Public Attributes
Communicator &	comm =*comm_fwd
	Communicator for plumed. More...

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

Communicator &	multi_sim_comm =*multi_sim_comm_fwd

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

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

TypesafePtr &	stopFlag =*stopFlag_fwd
	Stuff to make plumed stop the MD code cleanly. More...

bool	stopNow

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

Private Attributes
ActionSet &	actionSet =*actionSet_fwd
	Set of actions found in plumed.dat file. More...

ForwardDecl< ActionSet >	actionSet_fwd
	Forward declaration. More...

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

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

ForwardDecl< Atoms >	atoms_fwd
	Forward declaration. More...

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

Citations &	citations =*citations_fwd
	tools/Citations.holder More...

ForwardDecl< Citations >	citations_fwd
	Forward declaration. More...

std::unique_ptr< WithCmd >	cltool

ForwardDecl< Communicator >	comm_fwd
	Forward declaration. More...

DLLoader &	dlloader =*dlloader_fwd

ForwardDecl< DLLoader >	dlloader_fwd
	Forward declaration. More...

bool	doCheckPoint
	Flag for checkpointig. More...

bool	endPlumed
	End of input file. More...

plumed_error_handler	error_handler = {NULL,NULL}

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

ForwardDecl< ExchangePatterns >	exchangePatterns_fwd
	Forward declaration. More...

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

std::set< FileBase * >	files
	Pointers to files opened in actions associated to this object. More...

std::unique_ptr< WithCmd >	grex

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

Log &	log =*log_fwd
	Log stream. More...

ForwardDecl< Log >	log_fwd
	Forward declaration. More...

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

ForwardDecl< Communicator >	multi_sim_comm_fwd
	Forward declaration. More...

std::unique_ptr< DataFetchingObject >	mydatafetcher
	Object containing data we would like to grab and pass back. More...

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

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

bool	restart
	Flag for restart. More...

long int	step
	Present step number. More...

ForwardDecl< TypesafePtr >	stopFlag_fwd
	Forward declaration. More...

Stopwatch &	stopwatch =*stopwatch_fwd

ForwardDecl< Stopwatch >	stopwatch_fwd
	Forward declaration. More...

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

double	work
	The total work. 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()

◆ callErrorHandler()

bool PLMD::PlumedMain::callErrorHandler	(	int	code,
		const char *	msg
	)		const

inline

Call error handler.

Should only be called from plumed_plumedmain_cmd(). If the error handler was not set, returns false.

◆ cite()

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

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

◆ cmd() [1/6]

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

inlineinherited

◆ cmd() [2/6]

void PLMD::WithCmd::cmd

inline

◆ cmd() [3/6]

void PLMD::WithCmd::cmd	(	const std::string &	key,
		const TypesafePtr &	val,
		std::size_t	nelem,
		const std::size_t *	shape = `nullptr`
	)

inlineinherited

◆ cmd() [4/6]

void PLMD::WithCmd::cmd

inline

◆ cmd() [5/6]

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

overridevirtual

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.

◆ cmd() [6/6]

virtual void PLMD::WithCmd::cmd

◆ 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 std::vector< T > & v ) const

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

◆ getGoodNumThreads() [2/2]

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.

◆ 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().

◆ performCalcNoForces()

void PLMD::PlumedMain::performCalcNoForces ( )

Perform the calculation without backpropagation nor update() Shortcut for: waitData() + justCalculate()

◆ 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() [1/2]

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

Read an input file.

Parameters

str	name of the file

◆ readInputFile() [2/2]

void PLMD::PlumedMain::readInputFile ( IFile & ifile )

Read an input file.

Parameters

ifile

◆ 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

◆ readInputLines()

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

Read an input buffer.

Parameters

str	name of the string Same as readInputFile, but first write str on a temporary file and then read that files. At variance with readInputLine, it can take care of comments and continuation lines.

◆ 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 =*actionSet_fwd

private

Set of actions found in plumed.dat file.

◆ actionSet_fwd

ForwardDecl<ActionSet> PLMD::PlumedMain::actionSet_fwd

private

Forward declaration.

◆ 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 =*atoms_fwd

private

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

◆ atoms_fwd

ForwardDecl<Atoms> PLMD::PlumedMain::atoms_fwd

private

Forward declaration.

◆ bias

double PLMD::PlumedMain::bias

private

The total bias (=total energy of the restraints)

◆ citations

Citations& PLMD::PlumedMain::citations =*citations_fwd

private

tools/Citations.holder

◆ citations_fwd

ForwardDecl<Citations> PLMD::PlumedMain::citations_fwd

private

Forward declaration.

◆ cltool

std::unique_ptr<WithCmd> PLMD::PlumedMain::cltool

private

◆ comm

Communicator& PLMD::PlumedMain::comm =*comm_fwd

Communicator for plumed.

Includes all the processors used by plumed.

◆ comm_fwd

ForwardDecl<Communicator> PLMD::PlumedMain::comm_fwd

private

Forward declaration.

◆ detailedTimers

bool PLMD::PlumedMain::detailedTimers

Flag to switch on detailed timers.

◆ dlloader

DLLoader& PLMD::PlumedMain::dlloader =*dlloader_fwd

private

◆ dlloader_fwd

ForwardDecl<DLLoader> PLMD::PlumedMain::dlloader_fwd

private

Forward declaration.

◆ 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

◆ error_handler

plumed_error_handler PLMD::PlumedMain::error_handler = {NULL,NULL}

private

◆ exchangePatterns

ExchangePatterns& PLMD::PlumedMain::exchangePatterns =*exchangePatterns_fwd

private

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

◆ exchangePatterns_fwd

ForwardDecl<ExchangePatterns> PLMD::PlumedMain::exchangePatterns_fwd

private

Forward declaration.

◆ exchangeStep

bool PLMD::PlumedMain::exchangeStep

private

Set to true if on an exchange step.

◆ files

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

private

Pointers to files opened in actions associated to this object.

Notice that with the current implementation this should be at the top of this structure. Indeed, this should be destroyed after all the actions allocated in this PlumedMain object have been destroyed.

◆ grex

std::unique_ptr<WithCmd> PLMD::PlumedMain::grex

private

◆ initialized

bool PLMD::PlumedMain::initialized

private

Flag to avoid double initialization.

◆ log

Log& PLMD::PlumedMain::log =*log_fwd

private

Log stream.

◆ log_fwd

ForwardDecl<Log> PLMD::PlumedMain::log_fwd

private

Forward declaration.

◆ MDEngine

std::string PLMD::PlumedMain::MDEngine

private

Name of MD engine.

◆ multi_sim_comm

Communicator& PLMD::PlumedMain::multi_sim_comm =*multi_sim_comm_fwd

◆ multi_sim_comm_fwd

ForwardDecl<Communicator> PLMD::PlumedMain::multi_sim_comm_fwd

private

Forward declaration.

◆ mydatafetcher

std::unique_ptr<DataFetchingObject> PLMD::PlumedMain::mydatafetcher

private

Object containing data we would like to grab and pass back.

◆ 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

TypesafePtr& PLMD::PlumedMain::stopFlag =*stopFlag_fwd

Stuff to make plumed stop the MD code cleanly.

◆ stopFlag_fwd

ForwardDecl<TypesafePtr> PLMD::PlumedMain::stopFlag_fwd

private

Forward declaration.

◆ stopNow

bool PLMD::PlumedMain::stopNow

◆ stopwatch

Stopwatch& PLMD::PlumedMain::stopwatch =*stopwatch_fwd

private

◆ stopwatch_fwd

ForwardDecl<Stopwatch> PLMD::PlumedMain::stopwatch_fwd

private

Forward declaration.

Should be placed after log since its constructor takes a log reference as an argument.

◆ 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

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

Classes

Public Member Functions

Public Attributes

Private Attributes

Detailed Description

Constructor & Destructor Documentation

◆ PlumedMain()

◆ ~PlumedMain()

Member Function Documentation

◆ backwardPropagate()

◆ calc()

◆ callErrorHandler()

◆ cite()

◆ cmd() [1/6]

◆ cmd() [2/6]

◆ cmd() [3/6]

◆ cmd() [4/6]

◆ cmd() [5/6]

◆ cmd() [6/6]

◆ 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()

◆ performCalcNoForces()

◆ performCalcNoUpdate()

◆ prepareCalc()

◆ prepareDependencies()

◆ readInputFile() [1/2]

◆ readInputFile() [2/2]

◆ readInputLine()

◆ readInputLines()

◆ readInputWords()

◆ resetActive()

◆ runJobsAtEndOfCalculation()

◆ setEndPlumed()

◆ setExchangeStep()

◆ setRestart()

◆ setSuffix()

◆ shareData()

◆ stop()

◆ update()

◆ updateFlagsPop()

◆ updateFlagsPush()

◆ updateFlagsTop()

◆ waitData()

Member Data Documentation

◆ actionSet

◆ actionSet_fwd

◆ active

◆ atoms

◆ atoms_fwd

◆ bias

◆ citations

◆ citations_fwd

◆ cltool

◆ comm

◆ comm_fwd

◆ detailedTimers

◆ dlloader