Class for output files More...

#include <OFile.h>

Inheritance diagram for PLMD::OFile:

Classes
class	Field
	Class identifying a single field for fielded output. More...

Public Member Functions
	OFile ()
	Constructor. More...

	~OFile ()
	Destructor. More...

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

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

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

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

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

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

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

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

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

OFile &	addConstantField (const std::string &)

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

static void	test ()
	Runs a small testcase. More...

Protected Attributes
FILE *	fp
	file pointer More...

void *	gzfp
	zip file pointer. More...

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

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

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

bool	cloned
	Control closing on destructor. More...

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

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

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

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

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

Private Member Functions
size_t	llwrite (const char *, size_t)
	Low-level write. More...

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

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

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

char *	buffer_string
	Internal buffer for printf. More...

char *	buffer
	Internal buffer (generic use) More...

int	buflen
	Internal buffer length. More...

unsigned	actual_buffer_length
	This variables stores the actual buffer length. More...

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

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

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

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

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

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

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

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

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

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

Friends
template<class T >
OFile &	operator<< (OFile &, const T &)
	Formatted output with << operator. More...

Detailed Description

Class for output files

This class provides features similar to those in the standard C "FILE*" type, but only for sequential output. See IFile for sequential input.

See the example here for a possible use:

#include "File.h"

int main(){
  PLMD::OFile pof;
  pof.open("ciao");
  pof.printf("%s\n","test1");
  pof.setLinePrefix("plumed: ");
  pof.printf("%s\n","test2");
  pof.setLinePrefix("");
  pof.addConstantField("x2").printField("x2",67.0);
  pof.printField("x1",10.0).printField("x3",20.12345678901234567890).printField();
  pof.printField("x1",10.0).printField("x3",-1e70*20.12345678901234567890).printField();
  pof.printField("x3",10.0).printField("x2",777.0).printField("x1",-1e70*20.12345678901234567890).printField();
  pof.printField("x3",67.0).printField("x1",18.0).printField();
  pof.close();
  return 0;
}

This program is expected to produce a file "ciao" which reads

test1
plumed: test2
#! FIELDS x1 x3
#! SET x2                      67
                     10      20.12345678901234
                     10 -2.012345678901235e+71
#! FIELDS x1 x3
#! SET x2                     777
 -2.012345678901235e+71                     10
                     18                     67

Notes

"x2" is declared as "constant", which means that it is written using the "SET" keyword. Thus, everytime it is modified, all the headers are repeated in the output file.
printField() without arguments is used as a "newline".
most methods return a reference to the OFile itself, to allow chaining many calls on the same line (this is similar to << operator in std::ostream)

Using correctly OFile in PLUMED

When a OFile object is used in PLUMED it can be convenient to link() it to the Action object where it is defined, or to the PlumedMain object. This will save in the OFile a pointer to the linked object and will allow to have some extra information. E.g., if PLUMED is restarting, files will be appended. Notice that one can enforce this behavior using the enforceRestart() method before opening a file.

To have all files managed consistently, it is important to use OFile in the proper way. This should allow multi-replica plumed, restart and backups to work in the expected way. For this reason all the operations in OFile and IFile are synchronizing all the processors of the group, so call to OFile functions should always be performed by all processes; for this reason is also not usefull to use Log for debugging because only master threads will actually write. For debugging is better to use the standard stderr.

int main(){
// this is a growing file, containing a full history
// (frames are appended, as in traditional HILLS and COLVAR)
  OFile grw;
// this is a single-snapshopt file used e.g. for checkpointing
// (rewritten every time)
  OFile snp;

// open both files at the beginning
// (will go in \ref Action constructor)
  grw.open("growing");
  snp.open("snapshot");

// trajectory loop
  for(int i=0;i<nsteps;i++){

// files should be writen in the update() method of an \ref Action

// write on growing file
    grw<<"data at step "<<i<<\n";

// flushing
// it takes time, so do it only if data is critical
// better to leave this choice to the user with the FLUSH keyword
//    grw.flush();

// write on snapshot file
    snp.rewind();
    snp<<"snapshot at step "<<i<<"\n";
    snp.flush();
// the only difference is that snp is rewound
// notice that it should be rewound just before writing
// because rewind is going to move the file out of the way
// to have a safe copy of the file ("bck.last.filename")
// Also notice that snapshots should be flushed
// for this reason, it is better to write them only
// rarely to avoid excessive slow down

  }

  snp.close();
  grw.close();
}

Constructor & Destructor Documentation

◆ OFile()

PLMD::OFile::OFile ( )

Constructor.

◆ ~OFile()

PLMD::OFile::~OFile ( )

Destructor.

Member Function Documentation

◆ addConstantField()

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

◆ 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 )

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
	)

Backup a file by giving it a different name.

◆ checkRestart()

bool PLMD::OFile::checkRestart ( ) const

private

check if we are restarting

◆ clearFields()

OFile & PLMD::OFile::clearFields ( )

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 ( )

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

◆ enforceRestart()

OFile & PLMD::OFile::enforceRestart ( )

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

private

Find field index given name.

◆ flush()

FileBase & PLMD::OFile::flush ( )

virtual

Flush a file.

Reimplemented from PLMD::FileBase.

◆ fmtField() [1/2]

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

Set the format for writing double precision fields.

◆ fmtField() [2/2]

OFile & PLMD::OFile::fmtField ( )

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

◆ 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 ( FILE * fp )

inherited

Link to an already open filed.

◆ link() [2/9]

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

inherited

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

◆ link() [3/9]

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

inherited

Link to a Communicator object.

◆ link() [4/9]

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

inherited

Link to an Action object.

Automatically links also the corresponding PlumedMain and Communicator.

◆ link() [5/9]

FileBase & PLMD::FileBase::link

Allows overloading of link.

◆ link() [6/9]

FileBase & PLMD::FileBase::link

Allows overloading of link.

◆ link() [7/9]

FileBase & PLMD::FileBase::link

Allows overloading of link.

◆ link() [8/9]

FileBase & PLMD::FileBase::link

Allows overloading of link.

◆ link() [9/9]

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

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

◆ llwrite()

size_t PLMD::OFile::llwrite	(	const char *	ptr,
		size_t	s
	)

private

Low-level write.

◆ open() [1/2]

virtual FileBase& PLMD::FileBase::open

Allows overloading of open.

◆ open() [2/2]

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

virtual

Opens the file using automatic append/backup.

Implements PLMD::FileBase.

◆ operator bool()

PLMD::FileBase::operator bool ( ) const

inherited

Check for error/eof.

◆ printf()

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

Formatted output with explicit format - a la printf.

◆ printField() [1/5]

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

Set the value of a double precision field.

◆ printField() [2/5]

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

Set the value of a int field.

◆ printField() [3/5]

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

Set the value of a string field.

◆ printField() [4/5]

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

Print a value.

◆ printField() [5/5]

OFile & PLMD::OFile::printField ( )

Close a line.

Typically used as

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

◆ rewind()

OFile & PLMD::OFile::rewind ( )

Rewind a file.

◆ setBackupString()

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

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 )

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 )

Used to setup printing of values.

◆ test()

void PLMD::FileBase::test ( )

staticinherited

Runs a small testcase.

Friends And Related Function Documentation

◆ operator<<

template<class T >

OFile& operator<<	(	OFile &	of,
		const T &	t
	)

friend

Formatted output with << operator.

Member Data Documentation

◆ action

Action* PLMD::FileBase::action

protectedinherited

pointer to corresponding action. NULL if not linked

◆ actual_buffer_length

unsigned PLMD::OFile::actual_buffer_length

private

This variables stores the actual buffer length.

◆ backstring

std::string PLMD::OFile::backstring

private

The string used for backing up files.

◆ buffer

char* PLMD::OFile::buffer

private

Internal buffer (generic use)

◆ buffer_string

char* PLMD::OFile::buffer_string

private

Internal buffer for printf.

◆ buflen

int PLMD::OFile::buflen

private

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

private

All the defined constant fields.

◆ enforceBackup_

bool PLMD::OFile::enforceBackup_

private

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

◆ enforceRestart_

bool PLMD::OFile::enforceRestart_

private

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

private

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

private

Format for fields writing.

◆ fields

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

private

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

private

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

◆ linked

OFile* PLMD::OFile::linked

private

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

private

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

private

All the previously defined variable fields.

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

tools/OFile.h
tools/OFile.cpp

Classes

Public Member Functions

Static Public Member Functions

Protected Attributes

Private Member Functions

Private Attributes

Friends

Detailed Description

Using correctly OFile in PLUMED

Constructor & Destructor Documentation

◆ OFile()

◆ ~OFile()

Member Function Documentation

◆ addConstantField()

◆ appendSuffix()

◆ backupAllFiles()

◆ backupFile()

◆ checkRestart()

◆ clearFields()

◆ close()

◆ enforceBackup()

◆ enforceRestart()

◆ enforceSuffix()

◆ FileExist()

◆ findField()

◆ flush()

◆ fmtField() [1/2]

◆ fmtField() [2/2]

◆ 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() [1/5]

◆ printField() [2/5]

◆ printField() [3/5]

◆ printField() [4/5]

◆ printField() [5/5]

◆ rewind()

◆ setBackupString()

◆ setHeavyFlush()

◆ setLinePrefix()

◆ setupPrintValue()

◆ test()

Friends And Related Function Documentation

◆ operator<<

Member Data Documentation

◆ action

◆ actual_buffer_length

◆ backstring

◆ buffer

◆ buffer_string

◆ buflen

◆ cloned

◆ comm

◆ const_fields

◆ enforceBackup_

◆ enforceRestart_

◆ eof

◆ err

◆ fieldChanged

◆ fieldFmt

◆ fields

◆ fp

◆ gzfp

◆ heavyFlush

◆ linePrefix