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colvarproxy Class Reference

\brief Interface between the collective variables module and the simulation or analysis program (NAMD, VMD, LAMMPS...). This is the base class: each interfaced program is supported by a derived class. More...

#include <colvarproxy.h>

Inheritance diagram for colvarproxy:

List of all members.

Public Methods
	colvarproxy ()
	Constructor. More...
virtual	~colvarproxy ()
	Destructor. More...
virtual bool	io_available ()
	Ensure that we're on the main thread (derived class will do actual check). More...
virtual int	request_deletion ()
	Request deallocation of the module (currently only implemented by VMD). More...
bool	delete_requested ()
	Whether deallocation was requested. More...
virtual int	reset ()
	\brief Reset proxy state, e.g. requested atoms. More...
virtual int	parse_module_config ()
	(Re)initialize the module. More...
virtual int	setup ()
	(Re)initialize required member data (called after the module). More...
bool	engine_ready () const
	Whether the engine allows to fully initialize Colvars immediately. More...
void	add_config (std::string const &cmd, std::string const &conf)
	Enqueue new configuration text, to be parsed as soon as possible. More...
virtual int	update_input ()
	Update data required by Colvars module (e.g. read atom positions) TODO Break up colvarproxy_namd and colvarproxy_lammps function into these. More...
virtual int	update_output ()
	Update data based on the results of a Colvars call (e.g. send forces). More...
int	end_of_step ()
	Carry out operations needed before next simulation step is run. More...
virtual void	log (std::string const &message)
	Print a message to the main log. More...
virtual void	error (std::string const &message)
	Print a message to the main log and/or let the host code know about it. More...
void	add_error_msg (std::string const &message)
	Record error message (used by VMD to collect them after a script call). More...
std::string const &	get_error_msgs ()
	Retrieve accumulated error messages. More...
void	clear_error_msgs ()
	As the name says. More...
bool	simulation_running () const
	Whether a simulation is running (warn against irrecovarable errors). More...
bool	simulation_continuing () const
	Is the current step a repetition of a step just executed? This is set to true when the step 0 of a new "run" command is being executed, regardless of whether a state file has been loaded. More...
int	post_run ()
	Called at the end of a simulation segment (i.e. "run" command). More...
void	print_input_atomic_data ()
	Print a full list of all input atomic arrays for debug purposes. More...
void	print_output_atomic_data ()
	Print a full list of all applied forces for debug purposes. More...
int	get_version_from_string (char const *version_string)
	Convert a version string "YYYY-MM-DD" into an integer. More...
int	version_number () const
	Get the version number (higher = more recent). More...
Public Attributes
colvarmodule *	colvars
	Pointer to the main object. More...
Protected Attributes
bool	engine_ready_
	Whether the engine allows to fully initialize Colvars immediately. More...
std::string	error_output
	Collected error messages. More...
bool	b_simulation_running
	Whether a simulation is running (warn against irrecovarable errors). More...
bool	b_simulation_continuing
	Is the current step a repetition of a step just executed? This is set to true when the step 0 of a new "run" command is being executed, regardless of whether a state file has been loaded. More...
bool	b_delete_requested
	Whether the entire module should be deallocated by the host engine. More...
int	version_int
	Integer representing the version string (allows comparisons). More...
size_t	features_hash
	Track which features have been acknowledged during the last run. More...

Detailed Description

Definition at line 571 of file colvarproxy.h.

Constructor & Destructor Documentation

colvarproxy::colvarproxy ( )

Constructor.

Definition at line 460 of file colvarproxy.C.
References b_delete_requested, b_simulation_continuing, b_simulation_running, colvars, engine_ready_, features_hash, NULL, and version_int.

colvarproxy::~colvarproxy ( ) [virtual]

Destructor.

Definition at line 474 of file colvarproxy.C.
References colvarproxy_io::close_output_streams, colvars, and NULL.

Member Function Documentation

void colvarproxy::add_config ( std::string const & cmd,

std::string const & conf

)

Enqueue new configuration text, to be parsed as soon as possible.

Definition at line 509 of file colvarproxy.C.
References conf.

void colvarproxy::add_error_msg ( std::string const & message )

Record error message (used by VMD to collect them after a script call).

Definition at line 678 of file colvarproxy.C.
References error_output.
Referenced by colvarproxy_vmd::error.

void colvarproxy::clear_error_msgs ( )

As the name says.

Definition at line 688 of file colvarproxy.C.
References error_output.
Referenced by colvarmodule::clear_error.

bool colvarproxy::delete_requested ( ) [inline]

Whether deallocation was requested.

Definition at line 600 of file colvarproxy.h.
References b_delete_requested.

int colvarproxy::end_of_step ( )

Carry out operations needed before next simulation step is run.

Definition at line 556 of file colvarproxy.C.
References colvarproxy_system::cached_alch_lambda_changed, colvarproxy_atom_groups::compute_max_atom_groups_applied_force, colvarproxy_atoms::compute_max_atoms_applied_force, colvarproxy_volmaps::compute_max_volmaps_applied_force, colvarproxy_atom_groups::compute_rms_atom_groups_applied_force, colvarproxy_atoms::compute_rms_atoms_applied_force, colvarproxy_volmaps::compute_rms_volmaps_applied_force, colvarproxy_system::send_alch_lambda, colvarproxy_atoms::updated_charges_, and colvarproxy_atoms::updated_masses_.
Referenced by colvarmodule::calc.

bool colvarproxy::engine_ready ( ) const [inline]

Whether the engine allows to fully initialize Colvars immediately.

Definition at line 615 of file colvarproxy.h.
References engine_ready_.

void colvarproxy::error ( std::string const & message ) [virtual]

Print a message to the main log and/or let the host code know about it.

Reimplemented in colvarproxy_vmd.
Definition at line 671 of file colvarproxy.C.
References log.
Referenced by colvarmodule::error.

std::string const & colvarproxy::get_error_msgs ( )

Retrieve accumulated error messages.

Definition at line 694 of file colvarproxy.C.
References error_output.

int colvarproxy::get_version_from_string ( char const * version_string )

Convert a version string "YYYY-MM-DD" into an integer.

Definition at line 700 of file colvarproxy.C.
Referenced by colvarmodule::colvarmodule, colvarproxy_vmd::colvarproxy_vmd, and colvarmodule::read_restart.

bool colvarproxy::io_available ( ) [virtual]

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

Reimplemented from colvarproxy_io.
Definition at line 485 of file colvarproxy.C.
References colvarproxy_smp::smp_enabled, and colvarproxy_smp::smp_thread_id.

void colvarproxy::log ( std::string const & message ) [virtual]

Print a message to the main log.

Reimplemented in colvarproxy_vmd.
Definition at line 665 of file colvarproxy.C.
Referenced by error, and colvarmodule::log.

int colvarproxy::parse_module_config ( ) [virtual]

(Re)initialize the module.

Definition at line 521 of file colvarproxy.C.
References colvars, COLVARS_BUG_ERROR, colvarmodule::error, colvarmodule::read_config_file, and colvarmodule::read_config_string.

int colvarproxy::post_run ( )

Called at the end of a simulation segment (i.e. "run" command).

Definition at line 577 of file colvarproxy.C.
References colvars, colvarproxy_io::flush_output_streams, colvarmodule::output_prefix, colvarmodule::write_output_files, and colvarmodule::write_restart_file.

void colvarproxy::print_input_atomic_data ( )

Print a full list of all input atomic arrays for debug purposes.

Definition at line 589 of file colvarproxy.C.
References colvarproxy_atom_groups::atom_groups_charges, colvarproxy_atom_groups::atom_groups_coms, colvarproxy_atom_groups::atom_groups_ids, colvarproxy_atom_groups::atom_groups_masses, colvarproxy_atom_groups::atom_groups_refcount, colvarproxy_atom_groups::atom_groups_total_forces, colvarproxy_atoms::atoms_charges, colvarproxy_atoms::atoms_ids, colvarproxy_atoms::atoms_masses, colvarproxy_atoms::atoms_positions, colvarproxy_atoms::atoms_refcount, colvarproxy_atoms::atoms_total_forces, colvarmodule::log, colvarproxy_volmaps::volmaps_ids, and colvarproxy_volmaps::volmaps_values.

void colvarproxy::print_output_atomic_data ( )

Print a full list of all applied forces for debug purposes.

Definition at line 640 of file colvarproxy.C.
References colvarproxy_atom_groups::atom_groups_new_colvar_forces, colvarproxy_atoms::atoms_new_colvar_forces, colvarmodule::cv_prec, colvarmodule::cv_width, colvarmodule::log, and colvarproxy_volmaps::volmaps_new_colvar_forces.

int colvarproxy::request_deletion ( ) [virtual]

Request deallocation of the module (currently only implemented by VMD).

Reimplemented in colvarproxy_vmd.
Definition at line 501 of file colvarproxy.C.
References COLVARS_NOT_IMPLEMENTED, and colvarmodule::error.

int colvarproxy::reset ( ) [virtual]

\brief Reset proxy state, e.g. requested atoms.

Reimplemented from colvarproxy_atoms.
Definition at line 492 of file colvarproxy.C.
References colvarproxy_atom_groups::reset, and colvarproxy_atoms::reset.
Referenced by colvarmodule::reset.

int colvarproxy::setup ( ) [virtual]

(Re)initialize required member data (called after the module).

Reimplemented in colvarproxy_vmd.
Definition at line 515 of file colvarproxy.C.
Referenced by colvarproxy_vmd::setup.

bool colvarproxy::simulation_continuing ( ) const [inline]

Is the current step a repetition of a step just executed? This is set to true when the step 0 of a new "run" command is being executed, regardless of whether a state file has been loaded.

Definition at line 658 of file colvarproxy.h.
References b_simulation_continuing.
Referenced by colvarbias::can_accumulate_data.

bool colvarproxy::simulation_running ( ) const [inline]

Whether a simulation is running (warn against irrecovarable errors).

Definition at line 650 of file colvarproxy.h.
References b_simulation_running.
Referenced by colvarbias_abf::init, colvar::init_dependencies, colvarbias_restraint_k_moving::update, colvarbias_restraint_centers_moving::update, colvarbias_restraint_k_moving::update_acc_work, and colvarbias_restraint_centers_moving::update_acc_work.

int colvarproxy::update_input ( ) [virtual]

Update data required by Colvars module (e.g. read atom positions) TODO Break up colvarproxy_namd and colvarproxy_lammps function into these.

Reimplemented in colvarproxy_vmd.
Definition at line 544 of file colvarproxy.C.
Referenced by colvarproxy_vmd::update_input.

int colvarproxy::update_output ( ) [virtual]

Update data based on the results of a Colvars call (e.g. send forces).

Definition at line 550 of file colvarproxy.C.

int colvarproxy::version_number ( ) const [inline]

Get the version number (higher = more recent).

Definition at line 676 of file colvarproxy.h.
References version_int.

Member Data Documentation

bool colvarproxy::b_delete_requested [protected]

Whether the entire module should be deallocated by the host engine.

Definition at line 698 of file colvarproxy.h.
Referenced by colvarproxy, delete_requested, and colvarproxy_vmd::request_deletion.

bool colvarproxy::b_simulation_continuing [protected]

Is the current step a repetition of a step just executed? This is set to true when the step 0 of a new "run" command is being executed, regardless of whether a state file has been loaded.

Definition at line 695 of file colvarproxy.h.
Referenced by colvarproxy, and simulation_continuing.

bool colvarproxy::b_simulation_running [protected]

Whether a simulation is running (warn against irrecovarable errors).

Definition at line 690 of file colvarproxy.h.
Referenced by colvarproxy, colvarproxy_vmd::colvarproxy_vmd, and simulation_running.

colvarmodule* colvarproxy::colvars

Pointer to the main object.

Definition at line 586 of file colvarproxy.h.
Referenced by colvarproxy, colvarproxy_vmd::colvarproxy_vmd, colvarmodule::main, parse_module_config, post_run, colvarproxy_vmd::set_frame, colvarproxy_vmd::setup, and ~colvarproxy.

bool colvarproxy::engine_ready_ [protected]

Whether the engine allows to fully initialize Colvars immediately.

Definition at line 684 of file colvarproxy.h.
Referenced by colvarproxy, and engine_ready.

std::string colvarproxy::error_output [protected]

Collected error messages.

Definition at line 687 of file colvarproxy.h.
Referenced by add_error_msg, clear_error_msgs, and get_error_msgs.

size_t colvarproxy::features_hash [protected]

Track which features have been acknowledged during the last run.

Definition at line 704 of file colvarproxy.h.
Referenced by colvarproxy.

int colvarproxy::version_int [protected]

Integer representing the version string (allows comparisons).

Definition at line 701 of file colvarproxy.h.
Referenced by colvarproxy, colvarproxy_vmd::colvarproxy_vmd, and version_number.

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

Generated on Sun Sep 15 02:46:28 2024 for VMD (current) by

colvarproxy Class Reference

Public Methods

Public Attributes

Protected Attributes

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation