Files
lammps/lib/colvars/colvarproxy_io.h
Giacomo Fiorin 377c652a83 Update Colvars library to version 2023-05-01
This update consists exclusively of bugfixes or maintenance-related changes.

The following is a list of pull requests in the Colvars repository since the previous update to LAMMPS:

- 532 Add XYZ trajectory reading feature
  https://github.com/Colvars/colvars/pull/532 (@jhenin, @giacomofiorin)

- 531 Delete objects quietly, unless explicitly requested via script (including VMD)
  https://github.com/Colvars/colvars/pull/531 (@giacomofiorin)

- 530 Append newline to log and error messages if not already present
  https://github.com/Colvars/colvars/pull/530 (@giacomofiorin)

- 528 Forward-declare OpenMP lock
  https://github.com/Colvars/colvars/pull/528 (@giacomofiorin)

- 527 Remove unneeded STL container
  https://github.com/Colvars/colvars/pull/527 (@giacomofiorin)

- 526 Allow collecting configuration files and strings before setting up interface
  https://github.com/Colvars/colvars/pull/526 (@giacomofiorin, @jhenin)

- 523 Fallback to linearCombination when customFunction is missing in customColvar
  https://github.com/Colvars/colvars/pull/523 (@HanatoK, @giacomofiorin)

- 522 Use iostream::fail() to check for I/O error
  https://github.com/Colvars/colvars/pull/522 (@jhenin)

- 520 Fix ref count
  https://github.com/Colvars/colvars/pull/520 (@giacomofiorin)

- 513 Set target temperature through a common code path
  https://github.com/Colvars/colvars/pull/513 (@giacomofiorin, @jhenin)

- 509 Safer detection of Windows with recent Microsoft Visual Studio versions
  https://github.com/Colvars/colvars/pull/509 (@akohlmey)

- 508 Update LAMMPS patching method to reflect Lepton availability
  https://github.com/Colvars/colvars/pull/508 (@giacomofiorin)

- 497 Increase the precision of write_multicol
  https://github.com/Colvars/colvars/pull/497 (@HanatoK)

- 496 Only perform MTS automatic enable/disable for timeStepFactor > 1
  https://github.com/Colvars/colvars/pull/496 (@giacomofiorin)

- 493 Remove unused branch of quaternion input function
  https://github.com/Colvars/colvars/pull/493 (@giacomofiorin)

- 489 Ensure there are spaces between the fields in the header
  https://github.com/Colvars/colvars/pull/489 (@HanatoK)

- 487 Use map of output streams, and return references to its elements
  https://github.com/Colvars/colvars/pull/487 (@giacomofiorin, @jhenin)

- 486 Remember first step of moving restraint
  https://github.com/Colvars/colvars/pull/486 (@jhenin)

- 485 Add decoupling option for moving restraints
  https://github.com/Colvars/colvars/pull/485 (@jhenin)

- 483 Update Lepton via patching procedure
  https://github.com/Colvars/colvars/pull/483 (@giacomofiorin)

- 481 Make file-reading operations of input data abstractable
  https://github.com/Colvars/colvars/pull/481 (@giacomofiorin)

Authors: @akohlmey, @giacomofiorin, @HanatoK, @jhenin
2023-05-17 13:29:00 -04:00

168 lines
5.1 KiB
C++

// -*- c++ -*-
// This file is part of the Collective Variables module (Colvars).
// The original version of Colvars and its updates are located at:
// https://github.com/Colvars/colvars
// Please update all Colvars source files before making any changes.
// If you wish to distribute your changes, please submit them to the
// Colvars repository at GitHub.
#ifndef COLVARPROXY_IO_H
#define COLVARPROXY_IO_H
#include <map>
#include <string>
#include <iosfwd>
/// Methods for data input/output
class colvarproxy_io {
public:
/// Constructor
colvarproxy_io();
/// Destructor
virtual ~colvarproxy_io();
/// Ensure that we're on the main thread (derived class will do actual check)
virtual bool io_available();
/// \brief Save the current frame number in the argument given
// Returns error code
virtual int get_frame(long int &);
/// \brief Set the current frame number (as well as colvarmodule::it)
// Returns error code
virtual int set_frame(long int);
/// \brief Rename the given file, before overwriting it
virtual int backup_file(char const *filename);
/// \brief Rename the given file, before overwriting it
inline int backup_file(std::string const &filename)
{
return backup_file(filename.c_str());
}
/// Remove the given file (on Windows only, rename to filename.old)
virtual int remove_file(char const *filename);
/// Remove the given file (on Windows only, rename to filename.old)
inline int remove_file(std::string const &filename)
{
return remove_file(filename.c_str());
}
/// Rename the given file
virtual int rename_file(char const *filename, char const *newfilename);
/// Rename the given file
inline int rename_file(std::string const &filename,
std::string const &newfilename)
{
return rename_file(filename.c_str(), newfilename.c_str());
}
/// Prefix of the input state file to be read next
inline std::string & input_prefix()
{
return input_prefix_str;
}
/// Default prefix to be used for all output files (final configuration)
inline std::string & output_prefix()
{
return output_prefix_str;
}
/// Prefix of the restart (checkpoint) file to be written next
inline std::string & restart_output_prefix()
{
return restart_output_prefix_str;
}
/// Default restart frequency (as set by the simulation engine)
inline int default_restart_frequency() const
{
return restart_frequency_engine;
}
/// Buffer from which the input state information may be read
inline char const * & input_buffer()
{
return input_buffer_;
}
/// Returns a reference to given input stream, creating it if needed
/// \param input_name File name (later only a handle)
/// \param description Purpose of the file
/// \param error_on_fail Raise error when failing to open (allow testing)
virtual std::istream &input_stream(std::string const &input_name,
std::string const description = "file/channel",
bool error_on_fail = true);
/// Check if the file/channel is open (without opening it if not)
virtual bool input_stream_exists(std::string const &input_name);
/// Closes the given input stream
virtual int close_input_stream(std::string const &input_name);
/// Closes all input streams
virtual int close_input_streams();
/// Returns a reference to the named output file/channel (open it if needed)
/// \param output_name File name or identifier
/// \param description Purpose of the file
virtual std::ostream &output_stream(std::string const &output_name,
std::string const description = "file/channel");
/// Check if the file/channel is open (without opening it if not)
virtual bool output_stream_exists(std::string const &output_name);
/// Flushes the given output file/channel
virtual int flush_output_stream(std::string const &output_name);
/// Flushes all output files/channels
virtual int flush_output_streams();
/// Closes the given output file/channel
virtual int close_output_stream(std::string const &output_name);
/// Close all open files/channels to prevent data loss
virtual int close_output_streams();
protected:
/// Prefix of the input state file to be read next
std::string input_prefix_str;
/// Default prefix to be used for all output files (final configuration)
std::string output_prefix_str;
/// Prefix of the restart (checkpoint) file to be written next
std::string restart_output_prefix_str;
/// How often the simulation engine will write its own restart
int restart_frequency_engine;
/// Container of input files/channels indexed by path name
std::map<std::string, std::istream *> input_streams_;
/// Object whose reference is returned when read errors occur
std::istream *input_stream_error_;
/// Currently open output files/channels
std::map<std::string, std::ostream *> output_streams_;
/// Object whose reference is returned when write errors occur
std::ostream *output_stream_error_;
/// Buffer from which the input state information may be read
char const *input_buffer_;
};
#endif