Class containing the log stream. More...

#include <Log.h>

Inheritance diagram for PLMD::Log:

Public Member Functions
OFile &	addConstantField (const std::string &)

void	backupAllFiles (const std::string &str)
	This backs up all the files that would have been created with the name str. More...

void	backupFile (const std::string &bstring, const std::string &fname)
	Backup a file by giving it a different name. More...

OFile &	clearFields ()
	Resets the list of fields. More...

void	close ()
	Closes the file Should be used only for explicitely opened files. More...

OFile &	enforceBackup ()
	Enforce backup, even if the attached plumed object is restarting. More...

OFile &	enforceRestart ()
	Enforce restart, also if the attached plumed object is not restarting. More...

FileBase &	enforceSuffix (const std::string &suffix)
	Enforce suffix. More...

bool	FileExist (const std::string &path)
	Check if the file exists. More...

FileBase &	flush () override
	Flush a file. More...

OFile &	fmtField ()
	Reset the format for writing double precision fields to its default. More...

OFile &	fmtField (const std::string &)
	Set the format for writing double precision fields. More...

FILE *	getFILE () const
	Get the underlying file pointer. More...

std::string	getMode () const
	Retrieve the mode. More...

std::string	getPath () const
	Retrieve the path. More...

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

bool	isOpen ()
	Check if a file is open. More...

FileBase &	link (Action &)
	Link to an Action object. More...

FileBase &	link (Action &)
	Allows overloading of link. More...

FileBase &	link (Communicator &)
	Link to a Communicator object. More...

FileBase &	link (Communicator &)
	Allows overloading of link. More...

FileBase &	link (FILE *)
	Link to an already open filed. More...

FileBase &	link (FILE *)
	Allows overloading of link. More...

OFile &	link (OFile &)
	Allows linking this OFile to another one. More...

FileBase &	link (PlumedMain &)
	Link to a PlumedMain object Automatically links also the corresponding Communicator. More...

FileBase &	link (PlumedMain &)
	Allows overloading of link. More...

OFile &	open (const std::string &name) override
	Opens the file using automatic append/backup. More...

virtual FileBase &	open (const std::string &name)=0
	Allows overloading of open. More...

	operator bool () const
	Check for error/eof. More...

int	printf (const char *fmt,...)
	Formatted output with explicit format - a la printf. More...

OFile &	printField ()
	Close a line. More...

OFile &	printField (const std::string &, const std::string &)
	Set the value of a string field. More...

OFile &	printField (const std::string &, double)
	Set the value of a double precision field. More...

OFile &	printField (const std::string &, int)
	Set the value of a int type field. More...

OFile &	printField (const std::string &, long int)

OFile &	printField (const std::string &, long unsigned)

OFile &	printField (const std::string &, unsigned)

OFile &	printField (Value *val, const double &v)
	Print a value. More...

OFile &	rewind ()
	Rewind a file. More...

void	setBackupString (const std::string &)
	Set the string name to be used for automatic backup. More...

void	setHeavyFlush ()
	Set heavyFlush flag. More...

OFile &	setLinePrefix (const std::string &)
	Set the prefix for output. More...

OFile &	setupPrintValue (Value *val)
	Used to setup printing of values. More...

Static Public Member Functions
static std::string	appendSuffix (const std::string &path, const std::string &suffix)
	Append suffix. More...

Protected Attributes
Action *	action
	pointer to corresponding action. NULL if not linked More...

bool	cloned
	Control closing on destructor. More...

Communicator *	comm
	communicator. NULL if not set More...

bool	eof
	Set to true when end of file is encountered. More...

bool	err
	Set to true when error is encountered. More...

FILE *	fp
	file pointer More...

void *	gzfp
	zip file pointer. More...

bool	heavyFlush
	Set to true if you want flush to be heavy (close/reopen) More...

std::string	mode
	mode of the opened file More...

std::string	path
	path of the opened file More...

PlumedMain *	plumed
	pointer to main plumed object. NULL if not linked More...

Private Member Functions
bool	checkRestart () const
	check if we are restarting More...

unsigned	findField (const std::string &name) const
	Find field index given name. More...

std::size_t	llwrite (const char *, std::size_t)
	Low-level write. More...

Private Attributes
int	actual_buffer_length
	This variables stores the actual buffer length. More...

std::string	backstring
	The string used for backing up files. More...

std::unique_ptr< char[]>	buffer
	Internal buffer (generic use) More...

std::unique_ptr< char[]>	buffer_string
	Internal buffer for printf. More...

int	buflen
	Internal buffer length. More...

std::vector< Field >	const_fields
	All the defined constant fields. More...

bool	enforceBackup_
	True if backup behavior (i.e. non restart) should be forced. More...

std::string	enforcedSuffix
	Enforced suffix: More...

bool	enforcedSuffix_
	If true, use enforcedSuffix, else get it from PlumedMain. More...

bool	enforceRestart_
	True if restart behavior should be forced. More...

bool	fieldChanged
	True if fields has changed. More...

std::string	fieldFmt
	Format for fields writing. More...

std::vector< Field >	fields
	All the defined variable fields. More...

std::string	linePrefix
	Prefix for line (e.g. "PLUMED: ") More...

OFile *	linked
	Pointer to a linked OFile. More...

std::ostringstream	oss
	Temporary ostringstream for << output. More...

std::vector< Field >	previous_fields
	All the previously defined variable fields. More...

Detailed Description

Class containing the log stream.

It is similar to a FILE stream. It allows a printf() function, and also to write with a << operator. Moreover, it can prefix lines with the "PLUMED:" prefix, useful to grep out plumed log from output

Member Function Documentation

◆ addConstantField()

OFile & PLMD::OFile::addConstantField ( const std::string & name )

inherited

◆ appendSuffix()

std::string PLMD::FileBase::appendSuffix	(	const std::string &	path,
		const std::string &	suffix
	)

staticinherited

Append suffix.

It appends the desired suffix to the string. Notice that it conserves some suffix (e.g. gz/xtc/trr).

◆ backupAllFiles()

void PLMD::OFile::backupAllFiles ( const std::string & str )

inherited

This backs up all the files that would have been created with the name str.

It is used in analysis when you are not restarting. Analysis output files at different times, which are names analysis.0.<filename>, analysis.1.<filename> and <filename>, are backed up to bck.0.analysis.0.<filename>, bck.0.analysis.1.<filename> and bck.0.<filename>

◆ backupFile()

void PLMD::OFile::backupFile	(	const std::string &	bstring,
		const std::string &	fname
	)

inherited

Backup a file by giving it a different name.

◆ checkRestart()

bool PLMD::OFile::checkRestart ( ) const

privateinherited

check if we are restarting

◆ clearFields()

OFile & PLMD::OFile::clearFields ( )

inherited

Resets the list of fields.

As it is only possible to add new constant fields (addConstantField()), this method can be used to clean the field list.

◆ close()

void PLMD::FileBase::close ( )

inherited

Closes the file Should be used only for explicitely opened files.

◆ enforceBackup()

OFile & PLMD::OFile::enforceBackup ( )

inherited

Enforce backup, even if the attached plumed object is restarting.

◆ enforceRestart()

OFile & PLMD::OFile::enforceRestart ( )

inherited

Enforce restart, also if the attached plumed object is not restarting.

Useful for tests

◆ enforceSuffix()

FileBase & PLMD::FileBase::enforceSuffix ( const std::string & suffix )

inherited

Enforce suffix.

Overrides the one set in PlumedMain&

◆ FileExist()

bool PLMD::FileBase::FileExist ( const std::string & path )

inherited

Check if the file exists.

◆ findField()

unsigned PLMD::OFile::findField ( const std::string & name ) const

privateinherited

Find field index given name.

◆ flush()

FileBase & PLMD::OFile::flush ( )

overridevirtualinherited

Flush a file.

Reimplemented from PLMD::FileBase.

◆ fmtField() [1/2]

OFile & PLMD::OFile::fmtField ( )

inherited

Reset the format for writing double precision fields to its default.

◆ fmtField() [2/2]

OFile & PLMD::OFile::fmtField ( const std::string & fmt )

inherited

Set the format for writing double precision fields.

◆ getFILE()

FILE * PLMD::FileBase::getFILE ( ) const

inlineinherited

Get the underlying file pointer.

It might be null even if the file is open, e.g. when the file was open as a gzipped file.

◆ getMode()

std::string PLMD::FileBase::getMode ( ) const

inlineinherited

Retrieve the mode.

◆ getPath()

std::string PLMD::FileBase::getPath ( ) const

inlineinherited

Retrieve the path.

◆ getSuffix()

std::string PLMD::FileBase::getSuffix ( ) const

inherited

Get the file suffix.

◆ isOpen()

bool PLMD::FileBase::isOpen ( )

inherited

Check if a file is open.

◆ link() [1/9]

FileBase & PLMD::FileBase::link ( Action & action )

inherited

Link to an Action object.

Automatically links also the corresponding PlumedMain and Communicator.

◆ link() [2/9]

FileBase & PLMD::FileBase::link

inherited

Allows overloading of link.

◆ link() [3/9]

FileBase & PLMD::FileBase::link ( Communicator & comm )

inherited

Link to a Communicator object.

◆ link() [4/9]

FileBase & PLMD::FileBase::link

inherited

Allows overloading of link.

◆ link() [5/9]

FileBase & PLMD::FileBase::link ( FILE * fp )

inherited

Link to an already open filed.

◆ link() [6/9]

FileBase & PLMD::FileBase::link

inherited

Allows overloading of link.

◆ link() [7/9]

OFile & PLMD::OFile::link ( OFile & l )

inherited

Allows linking this OFile to another one.

In this way, everything written to this OFile will be immediately written on the linked OFile. Notice that a OFile should be either opened explicitly, linked to a FILE or linked to a OFile

◆ link() [8/9]

FileBase & PLMD::FileBase::link ( PlumedMain & plumed )

inherited

Link to a PlumedMain object Automatically links also the corresponding Communicator.

◆ link() [9/9]

FileBase & PLMD::FileBase::link

inherited

Allows overloading of link.

◆ llwrite()

size_t PLMD::OFile::llwrite	(	const char *	,
		std::size_t
	)

privateinherited

Low-level write.

◆ open() [1/2]

OFile & PLMD::OFile::open ( const std::string & name )

overridevirtualinherited

Opens the file using automatic append/backup.

Implements PLMD::FileBase.

◆ open() [2/2]

virtual FileBase& PLMD::FileBase::open

inherited

Allows overloading of open.

◆ operator bool()

PLMD::FileBase::operator bool ( ) const

inherited

Check for error/eof.

◆ printf()

int PLMD::OFile::printf	(	const char *	fmt,
			...
	)

inherited

Formatted output with explicit format - a la printf.

◆ printField() [1/8]

OFile & PLMD::OFile::printField ( )

inherited

Close a line.

Typically used as

  of.printField("a",a).printField("b",b).printField();

◆ printField() [2/8]

OFile & PLMD::OFile::printField	(	const std::string &	name,
		const std::string &	v
	)

inherited

Set the value of a string field.

◆ printField() [3/8]

OFile & PLMD::OFile::printField	(	const std::string &	name,
		double	v
	)

inherited

Set the value of a double precision field.

◆ printField() [4/8]

OFile & PLMD::OFile::printField	(	const std::string &	name,
		int	v
	)

inherited

Set the value of a int type field.

◆ printField() [5/8]

OFile & PLMD::OFile::printField	(	const std::string &	name,
		long int	v
	)

inherited

◆ printField() [6/8]

OFile & PLMD::OFile::printField	(	const std::string &	name,
		long unsigned	v
	)

inherited

◆ printField() [7/8]

OFile & PLMD::OFile::printField	(	const std::string &	name,
		unsigned	v
	)

inherited

◆ printField() [8/8]

OFile & PLMD::OFile::printField	(	Value *	val,
		const double &	v
	)

inherited

Print a value.

◆ rewind()

OFile & PLMD::OFile::rewind ( )

inherited

Rewind a file.

◆ setBackupString()

void PLMD::OFile::setBackupString ( const std::string & str )

inherited

Set the string name to be used for automatic backup.

◆ setHeavyFlush()

void PLMD::FileBase::setHeavyFlush ( )

inlineinherited

Set heavyFlush flag.

◆ setLinePrefix()

OFile & PLMD::OFile::setLinePrefix ( const std::string & l )

inherited

Set the prefix for output.

Typically "PLUMED: ". Notice that lines with a prefix cannot be parsed using fields in a IFile.

◆ setupPrintValue()

OFile & PLMD::OFile::setupPrintValue ( Value * val )

inherited

Used to setup printing of values.

Member Data Documentation

◆ action

Action* PLMD::FileBase::action

protectedinherited

pointer to corresponding action. NULL if not linked

◆ actual_buffer_length

int PLMD::OFile::actual_buffer_length

privateinherited

This variables stores the actual buffer length.

◆ backstring

std::string PLMD::OFile::backstring

privateinherited

The string used for backing up files.

◆ buffer

std::unique_ptr<char[]> PLMD::OFile::buffer

privateinherited

Internal buffer (generic use)

◆ buffer_string

std::unique_ptr<char[]> PLMD::OFile::buffer_string

privateinherited

Internal buffer for printf.

◆ buflen

int PLMD::OFile::buflen

privateinherited

Internal buffer length.

◆ cloned

bool PLMD::FileBase::cloned

protectedinherited

Control closing on destructor.

If true, file will not be closed in destructor

◆ comm

Communicator* PLMD::FileBase::comm

protectedinherited

communicator. NULL if not set

◆ const_fields

std::vector<Field> PLMD::OFile::const_fields

privateinherited

All the defined constant fields.

◆ enforceBackup_

bool PLMD::OFile::enforceBackup_

privateinherited

True if backup behavior (i.e. non restart) should be forced.

◆ enforcedSuffix

std::string PLMD::FileBase::enforcedSuffix

privateinherited

Enforced suffix:

◆ enforcedSuffix_

bool PLMD::FileBase::enforcedSuffix_

privateinherited

If true, use enforcedSuffix, else get it from PlumedMain.

◆ enforceRestart_

bool PLMD::OFile::enforceRestart_

privateinherited

True if restart behavior should be forced.

◆ eof

bool PLMD::FileBase::eof

protectedinherited

Set to true when end of file is encountered.

◆ err

bool PLMD::FileBase::err

protectedinherited

Set to true when error is encountered.

◆ fieldChanged

bool PLMD::OFile::fieldChanged

privateinherited

True if fields has changed.

This could be due to a change in the list of fields or a reset of a nominally constant field

◆ fieldFmt

std::string PLMD::OFile::fieldFmt

privateinherited

Format for fields writing.

◆ fields

std::vector<Field> PLMD::OFile::fields

privateinherited

All the defined variable fields.

◆ fp

FILE* PLMD::FileBase::fp

protectedinherited

file pointer

◆ gzfp

void* PLMD::FileBase::gzfp

protectedinherited

zip file pointer.

◆ heavyFlush

bool PLMD::FileBase::heavyFlush

protectedinherited

Set to true if you want flush to be heavy (close/reopen)

◆ linePrefix

std::string PLMD::OFile::linePrefix

privateinherited

Prefix for line (e.g. "PLUMED: ")

◆ linked

OFile* PLMD::OFile::linked

privateinherited

Pointer to a linked OFile.

see link(OFile&)

◆ mode

std::string PLMD::FileBase::mode

protectedinherited

mode of the opened file

◆ oss

std::ostringstream PLMD::OFile::oss

privateinherited

Temporary ostringstream for << output.

◆ path

std::string PLMD::FileBase::path

protectedinherited

path of the opened file

◆ plumed

PlumedMain* PLMD::FileBase::plumed

protectedinherited

pointer to main plumed object. NULL if not linked

◆ previous_fields

std::vector<Field> PLMD::OFile::previous_fields

privateinherited

All the previously defined variable fields.

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

tools/Log.h

Public Member Functions

Static Public Member Functions

Protected Attributes

Private Member Functions

Private Attributes

Detailed Description

Member Function Documentation

◆ addConstantField()

◆ appendSuffix()

◆ backupAllFiles()

◆ backupFile()

◆ checkRestart()

◆ clearFields()

◆ close()

◆ enforceBackup()

◆ enforceRestart()

◆ enforceSuffix()

◆ FileExist()

◆ findField()

◆ flush()

◆ fmtField() [1/2]

◆ fmtField() [2/2]

◆ getFILE()

◆ getMode()

◆ getPath()

◆ getSuffix()

◆ isOpen()

◆ link() [1/9]

◆ link() [2/9]

◆ link() [3/9]

◆ link() [4/9]

◆ link() [5/9]

◆ link() [6/9]

◆ link() [7/9]

◆ link() [8/9]

◆ link() [9/9]

◆ llwrite()

◆ open() [1/2]

◆ open() [2/2]

◆ operator bool()

◆ printf()

◆ printField() [1/8]

◆ printField() [2/8]

◆ printField() [3/8]

◆ printField() [4/8]

◆ printField() [5/8]

◆ printField() [6/8]

◆ printField() [7/8]

◆ printField() [8/8]

◆ rewind()

◆ setBackupString()

◆ setHeavyFlush()

◆ setLinePrefix()

◆ setupPrintValue()

Member Data Documentation

◆ action

◆ actual_buffer_length

◆ backstring

◆ buffer

◆ buffer_string

◆ buflen

◆ cloned

◆ comm

◆ const_fields

◆ enforceBackup_

◆ enforcedSuffix

◆ enforcedSuffix_

◆ enforceRestart_

◆ eof

◆ err

◆ fieldChanged

◆ fieldFmt

◆ fields

◆ fp

◆ gzfp

◆ heavyFlush

◆ linePrefix

◆ linked

◆ mode

◆ oss