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...

	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	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	calc ()
	Complete PLUMED calculation. More...

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

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

void	justApply ()
	Perform the backward loop on active actions. 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...

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...

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	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...

Private Types
typedef std::set< FileBase * > ::iterator	files_iterator

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...

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...

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...

std::set< FileBase * >	files

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

bool	stopNow

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.

Definition at line 71 of file PlumedMain.h.

Member Typedef Documentation

typedef std::set<FileBase*>::iterator PLMD::PlumedMain::files_iterator

private

Definition at line 132 of file PlumedMain.h.

Constructor & Destructor Documentation

PLMD::PlumedMain::PlumedMain ( )

Definition at line 51 of file PlumedMain.cpp.

PLMD::PlumedMain::~PlumedMain ( )

Definition at line 80 of file PlumedMain.cpp.

Member Function Documentation

void PLMD::PlumedMain::calc ( )

Complete PLUMED calculation.

Shortcut for prepareCalc() + performCalc()

Definition at line 434 of file PlumedMain.cpp.

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

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

Definition at line 652 of file PlumedMain.cpp.

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.

Definition at line 44 of file WithCmd.h.

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.

Definition at line 104 of file PlumedMain.cpp.

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

Erase a file.

Definition at line 666 of file PlumedMain.cpp.

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

Stop the run.

Definition at line 422 of file PlumedMain.cpp.

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

Closes a file opened with PlumedMain::fopen()

Definition at line 648 of file PlumedMain.cpp.

void PLMD::PlumedMain::fflush ( )

Flush all files.

Definition at line 656 of file PlumedMain.cpp.

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.

Definition at line 637 of file PlumedMain.cpp.

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

inline

Reference to the list of Action's.

Definition at line 283 of file PlumedMain.h.

Atoms & PLMD::PlumedMain::getAtoms ( )

inline

Reference to atoms object.

Definition at line 288 of file PlumedMain.h.

double PLMD::PlumedMain::getBias ( ) const

get the value of the bias

Definition at line 633 of file PlumedMain.cpp.

ExchangePatterns& PLMD::PlumedMain::getExchangePatterns ( )

inline

Access to exchange patterns.

Definition at line 276 of file PlumedMain.h.

bool PLMD::PlumedMain::getExchangeStep ( ) const

inline

Get exchangeStep flag.

Definition at line 313 of file PlumedMain.h.

Log & PLMD::PlumedMain::getLog ( )

Referenge to the log stream.

Definition at line 426 of file PlumedMain.cpp.

bool PLMD::PlumedMain::getRestart ( ) const

inline

Check if restarting.

Definition at line 303 of file PlumedMain.h.

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

inline

Return the number of the step.

Definition at line 235 of file PlumedMain.h.

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

inline

Get the suffix string.

Definition at line 293 of file PlumedMain.h.

void PLMD::PlumedMain::init ( )

Initialize the object.

Should be called once.

Definition at line 349 of file PlumedMain.cpp.

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

Insert a file.

Definition at line 662 of file PlumedMain.cpp.

void PLMD::PlumedMain::justApply ( )

Perform the backward loop on active actions.

Needed to apply the forces back.

Definition at line 548 of file PlumedMain.cpp.

void PLMD::PlumedMain::justCalculate ( )

Perform the forward loop on active actions.

Definition at line 508 of file PlumedMain.cpp.

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

Load a shared library.

Definition at line 601 of file PlumedMain.cpp.

void PLMD::PlumedMain::performCalc ( )

Perform the calculation.

Shortcut for waitData() + justCalculate() + justApply()

Definition at line 494 of file PlumedMain.cpp.

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()

Definition at line 439 of file PlumedMain.cpp.

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.

Definition at line 449 of file PlumedMain.cpp.

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

Read an input file.

Parameters

str	name of the file

Definition at line 378 of file PlumedMain.cpp.

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

Read an input string.

Parameters

str	name of the string

Definition at line 393 of file PlumedMain.cpp.

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.

Definition at line 318 of file PlumedMain.h.

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.

Definition at line 674 of file PlumedMain.cpp.

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

inline

Set exchangeStep flag.

Definition at line 308 of file PlumedMain.h.

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

inline

Set restart flag.

Definition at line 261 of file PlumedMain.h.

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

inline

Set the suffix string.

Definition at line 298 of file PlumedMain.h.

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.

Definition at line 486 of file PlumedMain.cpp.

void PLMD::PlumedMain::stop ( )

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

Definition at line 670 of file PlumedMain.cpp.

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.

Definition at line 500 of file PlumedMain.cpp.

Member Data Documentation

ActionSet& PLMD::PlumedMain::actionSet

private

Set of actions found in plumed.dat file.

Definition at line 110 of file PlumedMain.h.

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.

Definition at line 101 of file PlumedMain.h.

Atoms& PLMD::PlumedMain::atoms

private

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

Definition at line 107 of file PlumedMain.h.

double PLMD::PlumedMain::bias

private

The total bias (=total energy of the restraints)

Definition at line 120 of file PlumedMain.h.

Citations& PLMD::PlumedMain::citations

private

tools/Citations.holder

Definition at line 93 of file PlumedMain.h.

WithCmd* PLMD::PlumedMain::cltool

private

Definition at line 83 of file PlumedMain.h.

Communicator& PLMD::PlumedMain::comm

Communicator for plumed.

Includes all the processors used by plumed.

Definition at line 77 of file PlumedMain.h.

bool PLMD::PlumedMain::detailedTimers

Flag to switch on detailed timers.

Definition at line 143 of file PlumedMain.h.

DLLoader& PLMD::PlumedMain::dlloader

private

Definition at line 81 of file PlumedMain.h.

ExchangePatterns& PLMD::PlumedMain::exchangePatterns

private

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

Definition at line 123 of file PlumedMain.h.

bool PLMD::PlumedMain::exchangeStep

private

Set to true if on an exchange step.

Definition at line 126 of file PlumedMain.h.

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

private

Definition at line 131 of file PlumedMain.h.

WithCmd* PLMD::PlumedMain::grex

private

Definition at line 85 of file PlumedMain.h.

bool PLMD::PlumedMain::initialized

private

Flag to avoid double initialization.

Definition at line 87 of file PlumedMain.h.

Log& PLMD::PlumedMain::log

private

Log stream.

Definition at line 91 of file PlumedMain.h.

std::string PLMD::PlumedMain::MDEngine

private

Name of MD engine.

Definition at line 89 of file PlumedMain.h.

Communicator& PLMD::PlumedMain::multi_sim_comm

Definition at line 78 of file PlumedMain.h.

bool PLMD::PlumedMain::novirial

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

Definition at line 140 of file PlumedMain.h.

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

private

Set of Pilot actions.

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

Definition at line 114 of file PlumedMain.h.

std::string PLMD::PlumedMain::plumedDat

private

Name of the input file.

Definition at line 104 of file PlumedMain.h.

bool PLMD::PlumedMain::restart

private

Flag for restart.

Definition at line 129 of file PlumedMain.h.

long int PLMD::PlumedMain::step

private

Present step number.

Definition at line 96 of file PlumedMain.h.

int* PLMD::PlumedMain::stopFlag

private

Stuff to make plumed stop the MD code cleanly.

Definition at line 135 of file PlumedMain.h.

bool PLMD::PlumedMain::stopNow

private

Definition at line 136 of file PlumedMain.h.

Stopwatch& PLMD::PlumedMain::stopwatch

private

Definition at line 84 of file PlumedMain.h.

std::string PLMD::PlumedMain::suffix

private

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

Definition at line 117 of file PlumedMain.h.

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

core/PlumedMain.h
core/PlumedMain.cpp

Public Member Functions

Public Attributes

Private Types

Private Attributes

Detailed Description

Member Typedef Documentation

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation