Returns a reference to given input stream, creating it if needed
Parameters:

input_name File name (later only a handle)

description Purpose of the file

error_on_fail Raise error when failing to open (allow testing).

More...

virtual bool

input_stream_exists (std::string const &input_name)

Check if the file/channel is open (without opening it if not). More...

virtual int

close_input_stream (std::string const &input_name)

Closes the given input stream. More...

virtual int

close_input_streams ()

Closes all input streams. More...

virtual std::ostream &

output_stream (std::string const &output_name, std::string const description="file/channel")

Returns a reference to the named output file/channel (open it if needed)
Parameters:

output_name File name or identifier

description Purpose of the file.

More...

virtual bool

output_stream_exists (std::string const &output_name)

Check if the file/channel is open (without opening it if not). More...

virtual int

flush_output_stream (std::string const &output_name)

Flushes the given output file/channel. More...

virtual int

flush_output_streams ()

Flushes all output files/channels. More...

virtual int

close_output_stream (std::string const &output_name)

Closes the given output file/channel. More...

virtual int

close_output_streams ()

Close all open files/channels to prevent data loss. More...

Protected Attributes

std::string

input_prefix_str

Prefix of the input state file to be read next. More...

std::string

output_prefix_str

Default prefix to be used for all output files (final configuration). More...

std::string

restart_output_prefix_str

Prefix of the restart (checkpoint) file to be written next. More...

int

restart_frequency_engine

How often the simulation engine will write its own restart. More...

std::map< std::string, std::istream * >

input_streams_

Container of input files/channels indexed by path name. More...

std::istream *

input_stream_error_

Object whose reference is returned when read errors occur. More...

std::map< std::string, std::ostream * >

output_streams_

Currently open output files/channels. More...

std::ostream *

output_stream_error_

Object whose reference is returned when write errors occur. More...

char const *

input_buffer_

Buffer from which the input state information may be read. More...

Detailed Description

Methods for data input/output.

Definition at line 19 of file colvarproxy_io.h.

Constructor & Destructor Documentation

colvarproxy_io::colvarproxy_io ( )

Constructor.

Definition at line 30 of file colvarproxy_io.C.
References input_buffer_, input_stream_error_, NULL, output_stream_error_, and restart_frequency_engine.

colvarproxy_io::~colvarproxy_io ( ) [virtual]

Destructor.

Definition at line 41 of file colvarproxy_io.C.
References close_input_streams, close_output_streams, input_stream_error_, and output_stream_error_.

Member Function Documentation

int colvarproxy_io::backup_file ( std::string const & filename ) [inline]

\brief Rename the given file, before overwriting it.

Definition at line 44 of file colvarproxy_io.h.
References backup_file.

int colvarproxy_io::backup_file ( char const * filename ) [virtual]

\brief Rename the given file, before overwriting it.

Definition at line 68 of file colvarproxy_io.C.
References COLVARS_ERROR, colvarmodule::error, rename_file, and string.
Referenced by backup_file, colvarmodule::backup_file, and output_stream.

int colvarproxy_io::close_input_stream ( std::string const & input_name ) [virtual]

Closes the given input stream.

Definition at line 188 of file colvarproxy_io.C.
References COLVARS_FILE_ERROR, colvarmodule::error, input_stream_exists, and input_streams_.
Referenced by colvar_grid_gradient::colvar_grid_gradient, colvarbias_restraint_histogram::init, colvarmodule::read_config_file, UIestimator::UIestimator::read_inputfiles, colvar_grid::read_multicol, colvarbias::read_state_prefix, colvarmodule::setup_input, and simple_scalar_dist_functions.

int colvarproxy_io::close_input_streams ( ) [virtual]

Closes all input streams.

Definition at line 200 of file colvarproxy_io.C.
References input_streams_.
Referenced by ~colvarproxy_io.

int colvarproxy_io::close_output_stream ( std::string const & output_name ) [virtual]

Closes the given output file/channel.

Definition at line 279 of file colvarproxy_io.C.
References COLVARS_BUG_ERROR, colvarmodule::error, io_available, output_stream_exists, and output_streams_.
Referenced by colvarbias_meta::reopen_replica_buffer_file, colvar_grid::write_multicol, colvar_grid::write_opendx, colvarbias_restraint_histogram::write_output_files, colvarbias_meta::write_replica_state_file, colvarmodule::write_restart_file, and colvarbias_meta::~colvarbias_meta.

int colvarproxy_io::close_output_streams ( ) [virtual]

Close all open files/channels to prevent data loss.

Definition at line 296 of file colvarproxy_io.C.
References io_available, and output_streams_.
Referenced by colvarproxy::~colvarproxy, and ~colvarproxy_io.

int colvarproxy_io::default_restart_frequency ( ) const [inline]

Default restart frequency (as set by the simulation engine).

Definition at line 87 of file colvarproxy_io.h.
References restart_frequency_engine.
Referenced by colvarmodule::colvarmodule.

int colvarproxy_io::flush_output_stream ( std::string const & output_name ) [virtual]

Flushes the given output file/channel.

Definition at line 247 of file colvarproxy_io.C.
References io_available, output_stream_exists, and output_streams_.
Referenced by colvarbias_meta::replica_share, colvar::write_state, and colvarmodule::write_traj_files.

int colvarproxy_io::flush_output_streams ( ) [virtual]

Flushes all output files/channels.

Definition at line 263 of file colvarproxy_io.C.
References io_available, and output_streams_.
Referenced by colvarproxy::post_run, and colvarmodule::reset.

int colvarproxy_io::get_frame ( long int & ) [virtual]

\brief Save the current frame number in the argument given.

Reimplemented in colvarproxy_vmd.
Definition at line 56 of file colvarproxy_io.C.
References COLVARS_NOT_IMPLEMENTED.

char const* & colvarproxy_io::input_buffer ( ) [inline]

Buffer from which the input state information may be read.

Definition at line 93 of file colvarproxy_io.h.
References input_buffer_.
Referenced by colvarmodule::setup_input.

std::string& colvarproxy_io::input_prefix ( ) [inline]

Prefix of the input state file to be read next.

Definition at line 69 of file colvarproxy_io.h.
References input_prefix_str.
Referenced by colvarmodule::print_total_forces_errning, and colvarmodule::setup_input.

std::istream & colvarproxy_io::input_stream ( std::string const & input_name,

std::string const description = "file/channel",

bool error_on_fail = true

) [virtual]

Returns a reference to given input stream, creating it if needed
Parameters:

input_name File name (later only a handle)

description Purpose of the file

error_on_fail Raise error when failing to open (allow testing).

Definition at line 154 of file colvarproxy_io.C.
References COLVARS_BUG_ERROR, COLVARS_FILE_ERROR, colvarmodule::error, input_stream_error_, input_stream_exists, input_streams_, and io_available.
Referenced by colvar_grid_gradient::colvar_grid_gradient, colvarbias_restraint_histogram::init, colvarmodule::read_config_file, UIestimator::UIestimator::read_inputfiles, colvar_grid::read_multicol, colvarbias::read_state_prefix, colvarmodule::setup_input, and simple_scalar_dist_functions.

bool colvarproxy_io::input_stream_exists ( std::string const & input_name ) [virtual]

Check if the file/channel is open (without opening it if not).

Definition at line 182 of file colvarproxy_io.C.
References input_streams_.
Referenced by close_input_stream, and input_stream.

bool colvarproxy_io::io_available ( ) [virtual]

Ensure that we're on the main thread (derived class will do actual check).

Reimplemented in colvarproxy.
Definition at line 50 of file colvarproxy_io.C.
Referenced by close_output_stream, close_output_streams, flush_output_stream, flush_output_streams, input_stream, and output_stream.

std::string& colvarproxy_io::output_prefix ( ) [inline]

Default prefix to be used for all output files (final configuration).

Definition at line 75 of file colvarproxy_io.h.
References output_prefix_str.
Referenced by colvarmodule::setup_output.

std::ostream & colvarproxy_io::output_stream ( std::string const & output_name,

std::string const description = "file/channel"

) [virtual]

Returns a reference to the named output file/channel (open it if needed)
Parameters:

output_name File name or identifier

description Purpose of the file.

Definition at line 212 of file colvarproxy_io.C.
References backup_file, COLVARS_BUG_ERROR, COLVARS_FILE_ERROR, colvarmodule::debug, colvarmodule::error, io_available, colvarmodule::log, output_stream_error_, output_stream_exists, and output_streams_.
Referenced by colvar::calc_runave, colvarbias_meta::reopen_replica_buffer_file, colvar_grid::write_multicol, colvar_grid::write_opendx, colvarbias_restraint_histogram::write_output_files, colvarbias_meta::write_replica_state_file, colvarmodule::write_restart_file, and colvarmodule::write_traj_files.

bool colvarproxy_io::output_stream_exists ( std::string const & output_name ) [virtual]

Check if the file/channel is open (without opening it if not).

Definition at line 241 of file colvarproxy_io.C.
References output_streams_.
Referenced by colvar::calc_runave, close_output_stream, flush_output_stream, and output_stream.

int colvarproxy_io::remove_file ( std::string const & filename ) [inline]

Remove the given file (on Windows only, rename to filename.old).

Definition at line 53 of file colvarproxy_io.h.
References remove_file.

int colvarproxy_io::remove_file ( char const * filename ) [virtual]

Remove the given file (on Windows only, rename to filename.old).

Definition at line 100 of file colvarproxy_io.C.
References COLVARS_FILE_ERROR, and colvarmodule::error.
Referenced by remove_file, rename_file, colvarbias_meta::reopen_replica_buffer_file, and colvarbias_meta::write_replica_state_file.

int colvarproxy_io::rename_file ( std::string const & filename,

std::string const & newfilename

) [inline]

Rename the given file.

Definition at line 62 of file colvarproxy_io.h.
References rename_file.

int colvarproxy_io::rename_file ( char const * filename,

char const * newfilename

) [virtual]

Rename the given file.

Definition at line 133 of file colvarproxy_io.C.
References COLVARS_FILE_ERROR, colvarmodule::log, and remove_file.
Referenced by backup_file, rename_file, and colvarbias_meta::write_replica_state_file.

std::string& colvarproxy_io::restart_output_prefix ( ) [inline]

Prefix of the restart (checkpoint) file to be written next.

Definition at line 81 of file colvarproxy_io.h.
References restart_output_prefix_str.
Referenced by colvarmodule::setup_output.

int colvarproxy_io::set_frame ( long int ) [virtual]

\brief Set the current frame number (as well as colvarmodule::it).

Reimplemented in colvarproxy_vmd.
Definition at line 62 of file colvarproxy_io.C.
References COLVARS_NOT_IMPLEMENTED.

Member Data Documentation

char const* colvarproxy_io::input_buffer_ [protected]

Buffer from which the input state information may be read.

Definition at line 163 of file colvarproxy_io.h.
Referenced by colvarproxy_io, and input_buffer.

std::string colvarproxy_io::input_prefix_str [protected]

Prefix of the input state file to be read next.

Definition at line 139 of file colvarproxy_io.h.
Referenced by input_prefix.

std::istream* colvarproxy_io::input_stream_error_ [protected]

Object whose reference is returned when read errors occur.

Definition at line 154 of file colvarproxy_io.h.
Referenced by colvarproxy_io, input_stream, and ~colvarproxy_io.

std::map<std::string, std::istream *> colvarproxy_io::input_streams_ [protected]

Container of input files/channels indexed by path name.

Definition at line 151 of file colvarproxy_io.h.
Referenced by close_input_stream, close_input_streams, input_stream, and input_stream_exists.

std::string colvarproxy_io::output_prefix_str [protected]

Default prefix to be used for all output files (final configuration).

Definition at line 142 of file colvarproxy_io.h.
Referenced by output_prefix.

std::ostream* colvarproxy_io::output_stream_error_ [protected]

Object whose reference is returned when write errors occur.

Definition at line 160 of file colvarproxy_io.h.
Referenced by colvarproxy_io, output_stream, and ~colvarproxy_io.

std::map<std::string, std::ostream *> colvarproxy_io::output_streams_ [protected]

Currently open output files/channels.

Definition at line 157 of file colvarproxy_io.h.
Referenced by close_output_stream, close_output_streams, flush_output_stream, flush_output_streams, output_stream, and output_stream_exists.

int colvarproxy_io::restart_frequency_engine [protected]

How often the simulation engine will write its own restart.

Definition at line 148 of file colvarproxy_io.h.
Referenced by colvarproxy_io, and default_restart_frequency.

std::string colvarproxy_io::restart_output_prefix_str [protected]

Prefix of the restart (checkpoint) file to be written next.

Definition at line 145 of file colvarproxy_io.h.
Referenced by restart_output_prefix.

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

Generated on Tue Dec 3 02:47:19 2024 for VMD (current) by