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PLMD::OFile Class Reference

Class for output files. More...

#include <OFile.h>

Inheritance diagram for PLMD::OFile:
Inheritance graph
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Classes

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

Public Member Functions

 OFile ()
 Constructor. More...
 
 ~OFile ()
 Destructor. More...
 
OFilelink (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...
 
OFileopen (const std::string &name)
 Opens the file using automatic append/backup. More...
 
OFilesetLinePrefix (const std::string &)
 Set the prefix for output. More...
 
OFilefmtField (const std::string &)
 Set the format for writing double precision fields. More...
 
OFilefmtField ()
 Reset the format for writing double precision fields to its default. More...
 
OFileprintField (const std::string &, double)
 Set the value of a double precision field. More...
 
OFileprintField (const std::string &, int)
 Set the value of a int field. More...
 
OFileprintField (const std::string &, const std::string &)
 Set the value of a string field. More...
 
OFileaddConstantField (const std::string &)
 
OFilesetupPrintValue (Value *val)
 Used to setup printing of values. More...
 
OFileprintField (Value *val, const double &v)
 Print a value. More...
 
OFileprintField ()
 Close a line. More...
 
OFileclearFields ()
 Resets the list of fields. More...
 
int printf (const char *fmt,...)
 Formatted output with explicit format - a la printf. More...
 
OFilerewind ()
 Rewind a file. More...
 
virtual FileBaseflush ()
 Flush a file. More...
 
OFileenforceRestart ()
 Enforce restart, also if the attached plume object is not restarting. More...
 
FileBaselink (FILE *)
 Link to an already open filed. More...
 
FileBaselink (PlumedMain &)
 Link to a PlumedMain object Automatically links also the corresponding Communicator. More...
 
FileBaselink (Communicator &)
 Link to a Communicator object. More...
 
FileBaselink (Action &)
 Link to an Action object. 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...
 

Static Public Member Functions

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

Static Protected Member Functions

static std::string appendSuffix (const std::string &path, const std::string &suffix)
 Append suffix. More...
 

Protected Attributes

FILE * fp
 file pointer More...
 
void * gzfp
 zip file pointer. More...
 
Communicatorcomm
 communicator. NULL if not set More...
 
PlumedMainplumed
 pointer to main plumed object. NULL if not linked More...
 
Actionaction
 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...
 
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

OFilelinked
 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< Fieldprevious_fields
 All the previously defined variable fields. More...
 
std::vector< Fieldfields
 All the defined variable fields. More...
 
std::vector< Fieldconst_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...
 

Friends

template<class T >
OFileoperator<< (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

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.

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

PLMD::OFile::OFile ( )

Constructor.

PLMD::OFile::~OFile ( )

Destructor.

Member Function Documentation

OFile & PLMD::OFile::addConstantField ( const std::string &  name)
std::string PLMD::FileBase::appendSuffix ( const std::string &  path,
const std::string &  suffix 
)
staticprotectedinherited

Append suffix.

It appends the desired suffix to the string. Notice that it conserves a possible ".gz" suffix.

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>

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

Backup a file by giving it a different name.

bool PLMD::OFile::checkRestart ( ) const
private

check if we are restarting

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.

void PLMD::FileBase::close ( )
inherited

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

OFile & PLMD::OFile::enforceRestart ( )

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

Useful for tests

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

Check if the file exists.

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

Find field index given name.

FileBase & PLMD::OFile::flush ( )
virtual

Flush a file.

Reimplemented from PLMD::FileBase.

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

Set the format for writing double precision fields.

OFile & PLMD::OFile::fmtField ( )

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

bool PLMD::FileBase::isOpen ( )
inherited

Check if a file is open.

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

Link to an already open filed.

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

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

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

Link to a Communicator object.

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

Link to an Action object.

Automatically links also the corresponding PlumedMain and Communicator.

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

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

Low-level write.

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

Opens the file using automatic append/backup.

Implements PLMD::FileBase.

PLMD::FileBase::operator bool ( ) const
inherited

Check for error/eof.

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

Formatted output with explicit format - a la printf.

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

Set the value of a double precision field.

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

Set the value of a int field.

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

Set the value of a string field.

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

Print a value.

OFile & PLMD::OFile::printField ( )

Close a line.

Typically used as

  of.printField("a",a).printField("b",b).printField();
OFile & PLMD::OFile::rewind ( )

Rewind a file.

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

Set the string name to be used for automatic backup.

void PLMD::FileBase::setHeavyFlush ( )
inlineinherited

Set heavyFlush flag.

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.

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

Used to setup printing of values.

void PLMD::FileBase::test ( )
staticinherited

Runs a small testcase.

Friends And Related Function Documentation

template<class T >
OFile& operator<< ( OFile of,
const T &  t 
)
friend

Formatted output with << operator.

Member Data Documentation

Action* PLMD::FileBase::action
protectedinherited

pointer to corresponding action. NULL if not linked

unsigned PLMD::OFile::actual_buffer_length
private

This variables stores the actual buffer length.

std::string PLMD::OFile::backstring
private

The string used for backing up files.

char* PLMD::OFile::buffer
private

Internal buffer (generic use)

char* PLMD::OFile::buffer_string
private

Internal buffer for printf.

int PLMD::OFile::buflen
private

Internal buffer length.

bool PLMD::FileBase::cloned
protectedinherited

Control closing on destructor.

If true, file will not be closed in destructor

Communicator* PLMD::FileBase::comm
protectedinherited

communicator. NULL if not set

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

All the defined constant fields.

bool PLMD::OFile::enforceRestart_
private

True if restart behavior should be forced.

bool PLMD::FileBase::eof
protectedinherited

Set to true when end of file is encountered.

bool PLMD::FileBase::err
protectedinherited

Set to true when error is encountered.

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

std::string PLMD::OFile::fieldFmt
private

Format for fields writing.

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

All the defined variable fields.

FILE* PLMD::FileBase::fp
protectedinherited

file pointer

void* PLMD::FileBase::gzfp
protectedinherited

zip file pointer.

bool PLMD::FileBase::heavyFlush
protectedinherited

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

std::string PLMD::OFile::linePrefix
private

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

OFile* PLMD::OFile::linked
private

Pointer to a linked OFile.

see link(OFile&)

std::ostringstream PLMD::OFile::oss
private

Temporary ostringstream for << output.

std::string PLMD::FileBase::path
protectedinherited

path of the opened file

PlumedMain* PLMD::FileBase::plumed
protectedinherited

pointer to main plumed object. NULL if not linked

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: