colvarmodule Class Reference

Collective variables module (main class). More...

#include <colvarmodule.h>

List of all members.

Public Types
typedef double	real
	Defining an abstract real number allows to switch precision.
typedef int	residue_id
	Residue identifier.
typedef rvector	atom_pos
	Atom position (different type name from rvector, to make possible future PBC-transparent implementations).
typedef std::vector< atom >::iterator	atom_iter
typedef std::vector< atom >::const_iterator	atom_const_iter
Public Member Functions
	colvarmodule (char const *config_name, colvarproxy *proxy_in)
	Constructor.
	~colvarmodule ()
	Destructor.
void	init_colvars (std::string const &conf)
	Initialize collective variables.
void	init_biases (std::string const &conf)
	Initialize collective variable biases.
void	change_configuration (std::string const &bias_name, std::string const &conf)
real	energy_difference (std::string const &bias_name, std::string const &conf)
void	calc ()
	Calculate collective variables and biases.
std::istream &	read_restart (std::istream &is)
	Read the input restart file.
std::ostream &	write_restart (std::ostream &os)
	Write the output restart file.
void	write_output_files ()
	Write all output files (called by the proxy).
void	analyze ()
	Perform analysis.
bool	read_traj (char const *traj_filename, size_t traj_read_begin, size_t traj_read_end)
	Read a collective variable trajectory (post-processing only, not called at runtime).
Static Public Member Functions
size_t	step_relative ()
	Return the current step number from the beginning of this run.
size_t	step_absolute ()
bool	debug ()
	Whether debug output should be enabled (compile-time option).
void	backup_file (char const *filename)
	Call colvarproxy::backup_file().
colvar *	colvar_p (std::string const &name)
	Get the pointer of a colvar from its name (returns NULL if not found).
template<typename T>
std::string	to_str (T const &x, size_t const &width=0, size_t const &prec=0)
	Quick conversion of an object to a string.
template<typename T>
std::string	to_str (std::vector< T > const &x, size_t const &width=0, size_t const &prec=0)
	Quick conversion of a vector of objects to a string.
std::string	wrap_string (std::string const &s, size_t const &nchars)
	Reduce the number of characters in a string.
real	unit_angstrom ()
	Value of the unit for atomic coordinates with respect to angstroms (used by some variables for hard-coded default values).
real	boltzmann ()
	Boltmann constant.
real	temperature ()
	Temperature of the simulation (K).
real	dt ()
	Time step of MD integrator (fs).
void	request_system_force ()
	Request calculation of system force from MD engine.
void	log (std::string const &message)
	Print a message to the main log.
void	fatal_error (std::string const &message)
	Print a message to the main log and exit with error code.
void	exit (std::string const &message)
	Print a message to the main log and exit normally.
rvector	position_distance (atom_pos const &pos1, atom_pos const &pos2)
	Get the distance between two atomic positions with pbcs handled correctly.
real	position_dist2 (atom_pos const &pos1, atom_pos const &pos2)
	Get the square distance between two positions (with periodic boundary conditions handled transparently).
void	select_closest_image (atom_pos &pos, atom_pos const &ref_pos)
	Get the closest periodic image to a reference position.
void	select_closest_images (std::vector< atom_pos > &pos, atom_pos const &ref_pos)
	Perform select_closest_image() on a set of atomic positions.
void	load_atoms (char const *filename, std::vector< atom > &atoms, std::string const &pdb_field, double const pdb_field_value=0.0)
	Create atoms from a file.
void	load_coords (char const *filename, std::vector< atom_pos > &pos, const std::vector< int > &indices, std::string const &pdb_field, double const pdb_field_value=0.0)
	Load the coordinates for a group of atoms from a file (usually a PDB); the number of atoms in "filename" must match the number of elements in "pos".
real	rand_gaussian (void)
	Pseudo-random number with Gaussian distribution.
void	increase_depth ()
	Increase the depth (number of indentations in the output).
void	decrease_depth ()
	Decrease the depth (number of indentations in the output).
Public Attributes
bool	it_restart_from_state_file
std::string	restart_out_name
	Output restart file name.
Static Public Attributes
size_t	it = 0
	Current step number.
size_t	it_restart = 0
	Starting step number for this run.
real	debug_gradients_step_size = 1.0e-03
	Finite difference step size (if there is no dynamics, or if gradients need to be tested independently from the size of dt).
std::string	output_prefix = ""
	Prefix for all output files for this run.
std::string	input_prefix = ""
	Prefix for files from a previous run (including restart/output).
std::string	restart_in_name = ""
	input restart file name (determined from input_prefix)
std::vector< colvar * >	colvars
	Array of collective variables.
std::vector< colvarbias * >	biases
	Array of collective variable biases.
size_t	n_abf_biases = 0
	Number of ABF biases initialized (in normal conditions should be 1).
size_t	n_meta_biases = 0
	Number of metadynamics biases initialized (in normal conditions should be 1).
size_t	n_harm_biases = 0
	Number of harmonic biases initialized (no limit on the number).
size_t	n_histo_biases = 0
	Number of histograms initialized (no limit on the number).
size_t const	it_width = 12
	Number of characters to represent a time step.
size_t const	cv_prec = 14
	Number of digits to represent a collective variables value(s).
size_t const	cv_width = 21
	Number of characters to represent a collective variables value(s).
size_t const	en_prec = 14
	Number of digits to represent the collective variables energy.
size_t const	en_width = 21
	Number of characters to represent the collective variables energy.
std::string const	line_marker
	Line separator in the log output.
size_t	cv_traj_freq = 0
	Frequency for collective variables trajectory output.
bool	b_analysis = false
	True if only analysis is performed and not a run.
size_t	restart_out_freq = 0
	Frequency for saving output restarts.
Protected Attributes
std::ifstream	config_s
	Configuration file.
colvarparse *	parse
	Configuration file parser object.
std::string	cv_traj_name
	Name of the trajectory file.
std::ofstream	cv_traj_os
	Collective variables output trajectory file.
bool	cv_traj_append
	Appending to the existing trajectory file?
std::ofstream	restart_out_os
	Output restart file.
Static Protected Attributes
colvarproxy *	proxy = NULL
	Pointer to the proxy object, used to retrieve atomic data from the hosting program; it is static in order to be accessible from static functions in the colvarmodule class.
size_t	depth = 0
	Counter for the current depth in the object hierarchy (useg e.g. in outpu.
Friends
class	colvarproxy
class	atom
class	atom_group

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Detailed Description

Collective variables module (main class).

Class to control the collective variables calculation. An object (usually one) of this class is spawned from the MD program, containing all i/o routines and general interface.

At initialization, the colvarmodule object creates a proxy object to provide a transparent interface between the MD program and the child objects

Definition at line 47 of file colvarmodule.h.

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Member Typedef Documentation

typedef std::vector<atom>::const_iterator colvarmodule::atom_const_iter

Definition at line 85 of file colvarmodule.h.

typedef std::vector<atom>::iterator colvarmodule::atom_iter

Definition at line 84 of file colvarmodule.h.

typedef rvector colvarmodule::atom_pos

Atom position (different type name from rvector, to make possible future PBC-transparent implementations). Definition at line 74 of file colvarmodule.h. Referenced by colvarmodule::atom_group::calc_apply_roto_translation(), colvarmodule::atom_group::calc_fit_gradients(), colvar::eigenvector::calc_Jacobian_derivative(), colvar::rmsd::calc_Jacobian_derivative(), colvar::dihedral::calc_value(), colvar::angle::calc_value(), colvarmodule::atom_group::center_of_geometry(), colvarmodule::atom_group::center_of_mass(), colvarmodule::atom_group::center_ref_pos(), colvarproxy_namd::load_coords(), colvarmodule::atom_group::parse(), colvarproxy_namd::position_dist2(), position_dist2(), colvarproxy_namd::position_distance(), position_distance(), colvarmodule::atom::reset_data(), colvarproxy_namd::select_closest_image(), select_closest_image(), colvarproxy::select_closest_images(), and select_closest_images().

typedef double colvarmodule::real

Defining an abstract real number allows to switch precision. Definition at line 59 of file colvarmodule.h. Referenced by colvar::alpha_angles::apply_force(), colvar_grid_gradient::average(), colvar::calc(), colvarmodule::atom_group::calc_fit_gradients(), colvar::rmsd::calc_gradients(), colvar::gyration::calc_gradients(), colvar::distance_inv::calc_gradients(), colvar::gyration::calc_Jacobian_derivative(), colvar::calc_runave(), colvar::alpha_angles::calc_value(), colvar::rmsd::calc_value(), colvar::distance_inv::calc_value(), colvar::cvc::compare(), colvar::orientation::orientation(), colvarproxy_namd::position_dist2(), colvarbias_meta::project_hills(), colvarvalue::reset(), colvarbias_abf::update(), colvarbias_harmonic::update(), colvar::update(), colvar_grid_gradient::value_output(), colvar_grid_scalar::value_output(), colvar_grid_gradient::write_1D_integral(), and colvar::write_acf().

typedef int colvarmodule::residue_id

Residue identifier. Definition at line 61 of file colvarmodule.h.

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Constructor & Destructor Documentation

colvarmodule::colvarmodule (  char const *  config_name, colvarproxy *  proxy_in )

Constructor. Parameters: config_name  Configuration file name restart_name  (optional) Restart file name Definition at line 10 of file colvarmodule.C. References b_analysis, colvarproxy::backup_file(), colvarparse::check_keywords(), COLVARS_VERSION, config_s, cv_traj_append, cv_traj_freq, cv_traj_name, cv_traj_os, debug_gradients_step_size, fatal_error(), colvarparse::getline_nocomments(), init_biases(), init_colvars(), colvarproxy::input_prefix(), it, it_restart, it_restart_from_state_file, log(), colvarproxy::output_prefix(), output_prefix, parse, proxy, read_restart(), colvarproxy::restart_frequency(), restart_in_name, restart_out_freq, restart_out_name, and colvarproxy::restart_output_prefix(). { // pointer to the proxy object if (proxy == NULL) { proxy = proxy_in; parse = new colvarparse(); } else { cvm::fatal_error ("Error: trying to allocate twice the collective " "variable module.\n"); } cvm::log (cvm::line_marker); cvm::log ("Initializing the collective variables module, version "+ cvm::to_str(COLVARS_VERSION)+".\n"); // "it_restart" will be set by the input state file, if any; // "it" should be updated by the proxy it = it_restart = 0; it_restart_from_state_file = true; // open the configfile config_s.open (config_filename); if (!config_s) cvm::fatal_error ("Error: in opening configuration file \""+ std::string (config_filename)+"\".\n"); // read the config file into a string std::string conf = ""; { std::string line; while (colvarparse::getline_nocomments (config_s, line)) conf.append (line+"\n"); // don't need the stream any more config_s.close(); } parse->get_keyval (conf, "analysis", b_analysis, false); parse->get_keyval (conf, "debugGradientsStepSize", debug_gradients_step_size, 1.0e-07, colvarparse::parse_silent); parse->get_keyval (conf, "eigenvalueCrossingThreshold", colvarmodule::rotation::crossing_threshold, 1.0e-02, colvarparse::parse_silent); parse->get_keyval (conf, "colvarsTrajFrequency", cv_traj_freq, 100); parse->get_keyval (conf, "colvarsRestartFrequency", restart_out_freq, proxy->restart_frequency()); // by default overwrite the existing trajectory file parse->get_keyval (conf, "colvarsTrajAppend", cv_traj_append, false); // input restart file restart_in_name = proxy->input_prefix().size() ? std::string (proxy->input_prefix()+".colvars.state") : std::string ("") ; // output restart file restart_out_name = proxy->restart_output_prefix().size() ? std::string (proxy->restart_output_prefix()+".colvars.state") : std::string (""); if (restart_out_name.size()) cvm::log ("The restart output state file will be \""+restart_out_name+"\".\n"); output_prefix = proxy->output_prefix(); cvm::log ("The final output state file will be \""+ (output_prefix.size() ? std::string (output_prefix+".colvars.state") : std::string ("colvars.state"))+"\".\n"); cv_traj_name = (output_prefix.size() ? std::string (output_prefix+".colvars.traj") : std::string ("colvars.traj")); cvm::log ("The trajectory file will be \""+ cv_traj_name+"\".\n"); if (cv_traj_freq) { // open trajectory file if (cv_traj_append) { cvm::log ("Appending to colvar trajectory file \""+cv_traj_name+ "\".\n"); cv_traj_os.open (cv_traj_name.c_str(), std::ios::app); } else { proxy->backup_file (cv_traj_name.c_str()); cv_traj_os.open (cv_traj_name.c_str(), std::ios::out); } cv_traj_os.setf (std::ios::scientific, std::ios::floatfield); } // parse the options for collective variables init_colvars (conf); // parse the options for biases init_biases (conf); // done with the parsing, check that all keywords are valid parse->check_keywords (conf, "colvarmodule"); cvm::log (cvm::line_marker); // read the restart configuration, if available if (restart_in_name.size()) { // read the restart file std::ifstream input_is (restart_in_name.c_str()); if (!input_is.good()) fatal_error ("Error: in opening restart file \""+ std::string (restart_in_name)+"\".\n"); else { cvm::log ("Restarting from file \""+restart_in_name+"\".\n"); read_restart (input_is); cvm::log (cvm::line_marker); } } // check if it is possible to save output configuration if ((!output_prefix.size()) && (!restart_out_name.size())) { cvm::fatal_error ("Error: neither the final output state file or " "the output restart file could be defined, exiting.\n"); } cvm::log ("Collective variables module initialized.\n"); cvm::log (cvm::line_marker); }

colvarmodule::~colvarmodule (   )

Destructor. Definition at line 546 of file colvarmodule.C. References biases, colvars, and cv_traj_os. { for (std::vector<colvar *>::iterator cvi = colvars.begin(); cvi != colvars.end(); cvi++) { delete *cvi; } colvars.clear(); for (std::vector<colvarbias *>::iterator bi = biases.begin(); bi != biases.end(); bi++) { delete *bi; } biases.clear(); if (cv_traj_os.good()) { cv_traj_os.close(); } delete parse; }

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Member Function Documentation

void colvarmodule::analyze (   )

Perform analysis. Definition at line 516 of file colvarmodule.C. References biases, colvars, debug(), decrease_depth(), increase_depth(), it, log(), and step_relative(). { if (cvm::debug()) { cvm::log ("colvarmodule::analyze(), step = "+cvm::to_str (it)+".\n"); } if (cvm::step_relative() == 0) cvm::log ("Performing analysis.\n"); // perform colvar-specific analysis for (std::vector<colvar *>::iterator cvi = colvars.begin(); cvi != colvars.end(); cvi++) { cvm::increase_depth(); (*cvi)->analyse(); cvm::decrease_depth(); } // perform bias-specific analysis for (std::vector<colvarbias *>::iterator bi = biases.begin(); bi != biases.end(); bi++) { cvm::increase_depth(); (*bi)->analyse(); cvm::decrease_depth(); } }

void cvm::backup_file (  char const *  filename  )  [inline, static]

Call colvarproxy::backup_file(). Definition at line 479 of file colvarmodule.h. References colvarproxy::backup_file(), and proxy. Referenced by colvarbias_meta::write_pmf(), and colvarbias_meta::write_replica_state_file(). { proxy->backup_file (filename); }

cvm::real cvm::boltzmann (   )  [inline, static]

Boltmann constant. Definition at line 418 of file colvarmodule.h. References colvarproxy::boltzmann(), and proxy. Referenced by colvar::colvar(), and colvar::update(). { return proxy->boltzmann(); }

void colvarmodule::calc (   )

Calculate collective variables and biases. Definition at line 339 of file colvarmodule.C. References colvarproxy::add_energy(), colvarproxy::backup_file(), biases, colvars, cv_traj_freq, cv_traj_name, cv_traj_os, debug(), decrease_depth(), fatal_error(), increase_depth(), it, log(), proxy, restart_out_freq, restart_out_name, restart_out_os, step_absolute(), step_relative(), wrap_string(), and write_restart(). Referenced by colvarproxy_namd::calculate(). { cvm::real total_bias_energy = 0.0; cvm::real total_colvar_energy = 0.0; if (cvm::debug()) { cvm::log (cvm::line_marker); cvm::log ("Collective variables module, step no. "+ cvm::to_str (cvm::step_absolute())+"\n"); } // calculate collective variables and their gradients if (cvm::debug()) cvm::log ("Calculating collective variables.\n"); cvm::increase_depth(); for (std::vector<colvar *>::iterator cvi = colvars.begin(); cvi != colvars.end(); cvi++) { (*cvi)->calc(); } cvm::decrease_depth(); // update the biases and communicate their forces to the collective // variables if (cvm::debug() && biases.size()) cvm::log ("Updating collective variable biases.\n"); cvm::increase_depth(); for (std::vector<colvarbias *>::iterator bi = biases.begin(); bi != biases.end(); bi++) { total_bias_energy += (*bi)->update(); } cvm::decrease_depth(); // sum the forces from all biases for each collective variable if (cvm::debug() && biases.size()) cvm::log ("Collecting forces from all biases.\n"); cvm::increase_depth(); for (std::vector<colvar *>::iterator cvi = colvars.begin(); cvi != colvars.end(); cvi++) { (*cvi)->reset_bias_force(); } for (std::vector<colvarbias *>::iterator bi = biases.begin(); bi != biases.end(); bi++) { (*bi)->communicate_forces(); } cvm::decrease_depth(); if (cvm::b_analysis) { // perform runtime analysis of colvars and biases if (cvm::debug() && biases.size()) cvm::log ("Perform runtime analyses.\n"); cvm::increase_depth(); for (std::vector<colvar *>::iterator cvi = colvars.begin(); cvi != colvars.end(); cvi++) { (*cvi)->analyse(); } for (std::vector<colvarbias *>::iterator bi = biases.begin(); bi != biases.end(); bi++) { (*bi)->analyse(); } cvm::decrease_depth(); } // sum up the forces for each colvar and integrate any internal // equation of motion if (cvm::debug()) cvm::log ("Updating the internal degrees of freedom " "of colvars (if they have any).\n"); cvm::increase_depth(); for (std::vector<colvar *>::iterator cvi = colvars.begin(); cvi != colvars.end(); cvi++) { total_colvar_energy += (*cvi)->update(); } cvm::decrease_depth(); proxy->add_energy (total_bias_energy + total_colvar_energy); // make collective variables communicate their forces to their // coupled degrees of freedom (i.e. atoms) if (cvm::debug()) cvm::log ("Communicating forces from the colvars to the atoms.\n"); cvm::increase_depth(); for (std::vector<colvar *>::iterator cvi = colvars.begin(); cvi != colvars.end(); cvi++) { if ((*cvi)->tasks[colvar::task_gradients]) (*cvi)->communicate_forces(); } cvm::decrease_depth(); // write restart file, if needed if (restart_out_freq && restart_out_name.size() && !cvm::b_analysis) { if ( (cvm::step_relative() > 0) && ((cvm::step_absolute() % restart_out_freq) == 0) ) { cvm::log ("Writing the state file \""+ restart_out_name+"\".\n"); proxy->backup_file (restart_out_name.c_str()); restart_out_os.open (restart_out_name.c_str()); restart_out_os.setf (std::ios::scientific, std::ios::floatfield); if (!write_restart (restart_out_os)) cvm::fatal_error ("Error: in writing restart file.\n"); restart_out_os.close(); } } // write trajectory file, if needed if (cv_traj_freq) { if (cvm::debug()) cvm::log ("Writing trajectory file.\n"); // (re)open trajectory file if (!cv_traj_os.good()) { if (cv_traj_append) { cvm::log ("Appending to colvar trajectory file \""+cv_traj_name+ "\".\n"); cv_traj_os.open (cv_traj_name.c_str(), std::ios::app); } else { cvm::log ("Overwriting colvar trajectory file \""+cv_traj_name+ "\".\n"); proxy->backup_file (cv_traj_name.c_str()); cv_traj_os.open (cv_traj_name.c_str(), std::ios::out); } cv_traj_os.setf (std::ios::scientific, std::ios::floatfield); } // write labels in the traj file every 1000 lines and at first ts cvm::increase_depth(); if ((cvm::step_absolute() % (cv_traj_freq * 1000)) == 0 || cvm::step_relative() == 0) { cv_traj_os << "# " << cvm::wrap_string ("step", cvm::it_width-2) << " "; if (cvm::debug()) cv_traj_os.flush(); for (std::vector<colvar *>::iterator cvi = colvars.begin(); cvi != colvars.end(); cvi++) { (*cvi)->write_traj_label (cv_traj_os); } cv_traj_os << "\n"; if (cvm::debug()) cv_traj_os.flush(); } cvm::decrease_depth(); // write collective variable values to the traj file cvm::increase_depth(); if ((cvm::step_absolute() % cv_traj_freq) == 0) { cv_traj_os << std::setw (cvm::it_width) << it << " "; for (std::vector<colvar *>::iterator cvi = colvars.begin(); cvi != colvars.end(); cvi++) { (*cvi)->write_traj (cv_traj_os); } cv_traj_os << "\n"; if (cvm::debug()) cv_traj_os.flush(); } cvm::decrease_depth(); if (restart_out_freq) { // flush the trajectory file if we are at the restart frequency if ( (cvm::step_relative() > 0) && ((cvm::step_absolute() % restart_out_freq) == 0) ) { cvm::log ("Synchronizing (emptying the buffer of) trajectory file \""+ cv_traj_name+"\".\n"); cv_traj_os.flush(); } } } // end if (cv_traj_freq) }

void colvarmodule::change_configuration (  std::string const &  bias_name, std::string const &  conf )

Load new configuration for the given bias - currently works for harmonic (force constant and/or centers) Definition at line 300 of file colvarmodule.C. References biases, decrease_depth(), fatal_error(), and increase_depth(). { cvm::increase_depth(); int found = 0; for (std::vector<colvarbias *>::iterator bi = biases.begin(); bi != biases.end(); bi++) { if ( (*bi)->name == bias_name ) { ++found; (*bi)->change_configuration (conf); } } if (found < 1) cvm::fatal_error ("Error: bias not found.\n"); if (found > 1) cvm::fatal_error ("Error: duplicate bias name.\n"); cvm::decrease_depth(); }

colvar * cvm::colvar_p (  std::string const &  name  )  [inline, static]

Get the pointer of a colvar from its name (returns NULL if not found). Definition at line 524 of file colvar.h. Referenced by colvarbias::add_colvar(), colvar::calc_acf(), and colvar::parse_analysis(). { for (std::vector<colvar *>::iterator cvi = cvm::colvars.begin(); cvi != cvm::colvars.end(); cvi++) { if ((*cvi)->name == name) { return (*cvi); } } return NULL; }

bool colvarmodule::debug (   )  [inline, static]

Whether debug output should be enabled (compile-time option). Definition at line 152 of file colvarmodule.h. Referenced by colvarbias::add_colvar(), colvar_grid< size_t >::address(), colvar::alpha_angles::alpha_angles(), analyze(), colvarmodule::atom::atom(), colvar::build_atom_list(), calc(), colvar::calc(), colvarmodule::atom_group::calc_fit_gradients(), colvar::calc_runave(), colvar::alpha_angles::calc_value(), colvarproxy_namd::calculate(), colvarparse::check_keywords(), colvar::colvar(), colvar_grid< size_t >::colvar_grid(), colvarbias_harmonic::colvarbias_harmonic(), colvarbias_meta::colvarbias_meta(), colvarproxy_namd::colvarproxy_namd(), colvarbias::communicate_forces(), colvar::communicate_forces(), colvarbias_meta::create_hill(), colvar::cvc::cvc(), colvarbias_meta::delete_hill(), colvar::dihedPC::dihedPC(), colvar::dihedral::dihedral(), colvar::enable(), colvarproxy_namd::fatal_error(), colvar::h_bond::h_bond(), colvarbias_meta::hill::hill(), init_biases(), init_colvars(), colvar_grid< size_t >::map_grid(), colvarmodule::atom_group::parse(), colvarbias_meta::project_hills(), colvarbias_meta::read_hill(), colvarbias_meta::read_replica_files(), colvarbias_meta::read_restart(), colvarbias_meta::update(), colvarbias_histogram::update(), colvarbias_abf::update(), colvarbias_harmonic::update(), colvar::update(), and colvarbias_meta::update_replicas_registry(). { return COLVARS_DEBUG; }

void cvm::decrease_depth (   )  [static]

Decrease the depth (number of indentations in the output). Definition at line 707 of file colvarmodule.C. References depth. Referenced by analyze(), calc(), colvar::calc(), change_configuration(), colvar::communicate_forces(), energy_difference(), init_biases(), init_colvars(), colvarmodule::atom_group::parse(), read_restart(), colvar::update(), write_output_files(), and write_restart(). { if (depth) depth--; }

cvm::real cvm::dt (   )  [inline, static]

Time step of MD integrator (fs). Definition at line 428 of file colvarmodule.h. References colvarproxy::dt(), and proxy. Referenced by colvar::fdiff_velocity(), colvar::update(), and write_restart(). { return proxy->dt(); }

cvm::real colvarmodule::energy_difference (  std::string const &  bias_name, std::string const &  conf )

Calculate change in energy from using alt. config. for the given bias - currently works for harmonic (force constant and/or centers) Definition at line 318 of file colvarmodule.C. References biases, decrease_depth(), fatal_error(), and increase_depth(). { cvm::increase_depth(); cvm::real energy_diff = 0.; int found = 0; for (std::vector<colvarbias *>::iterator bi = biases.begin(); bi != biases.end(); bi++) { if ( (*bi)->name == bias_name ) { ++found; energy_diff = (*bi)->energy_difference (conf); } } if (found < 1) cvm::fatal_error ("Error: bias not found.\n"); if (found > 1) cvm::fatal_error ("Error: duplicate bias name.\n"); cvm::decrease_depth(); return energy_diff; }

void cvm::exit (  std::string const &  message  )  [static]

Print a message to the main log and exit normally. Definition at line 717 of file colvarmodule.C. References colvarproxy::exit(), and proxy. { proxy->exit (message); }

void cvm::fatal_error (  std::string const &  message  )  [static]

Print a message to the main log and exit with error code. Definition at line 712 of file colvarmodule.C. References colvarproxy::fatal_error(), and proxy. Referenced by colvarmodule::atom_group::add_atom(), colvarbias::add_colvar(), colvar_grid< size_t >::add_grid(), colvar_grid< size_t >::address(), colvar::alpha_angles::alpha_angles(), colvarmodule::atom_group::apply_colvar_force(), colvarmodule::atom_group::apply_force(), colvarmodule::atom_group::apply_forces(), colvarmodule::atom::atom(), calc(), colvar::calc_acf(), colvar::cvc::calc_force_invgrads(), colvar::cvc::calc_Jacobian_derivative(), colvarproxy_namd::calculate(), change_configuration(), colvarbias::change_configuration(), colvar_grid< size_t >::check_consistency(), colvarparse::check_keywords(), colvarvalue::check_types(), colvar::colvar(), colvar_grid< size_t >::colvar_grid(), colvarbias::colvarbias(), colvarbias_abf::colvarbias_abf(), colvarbias_harmonic::colvarbias_harmonic(), colvarbias_histogram::colvarbias_histogram(), colvarbias_meta::colvarbias_meta(), colvarmodule(), colvar::orientation::compare(), colvar::distance_dir::compare(), colvar::distance_vec::compare(), colvar::cvc::compare(), colvar::coordnum::coordnum(), colvar_grid< size_t >::create(), colvarmodule::atom_group::create_sorted_ids(), colvar::dihedPC::dihedPC(), colvar::distance_inv::distance_inv(), colvar::distance_z::distance_z(), colvar::eigenvector::eigenvector(), colvar::enable(), energy_difference(), colvarbias::energy_difference(), colvarvalue::error_lside(), colvarvalue::error_rside(), colvar_grid_scalar::gradient_finite_diff(), colvar::h_bond::h_bond(), colvar::inertia_z::inertia_z(), init_colvars(), jacobi(), colvarparse::key_lookup(), colvarproxy_namd::load_atoms(), colvarproxy_namd::load_coords(), colvar_grid< size_t >::map_grid(), operator>>(), colvarmodule::quaternion::operator[](), colvar::orientation::orientation(), colvarvalue::p2leg_opt(), colvarmodule::atom_group::parse(), colvar::parse_analysis(), colvar::cvc::parse_group(), colvar_grid< size_t >::parse_params(), pdb_field_str2enum(), colvar::periodic_boundaries(), colvarmodule::atom_group::positions(), colvarmodule::atom_group::positions_shifted(), colvarbias_meta::read_hill(), colvar_grid< size_t >::read_multicol(), colvar_grid< size_t >::read_raw_error(), read_restart(), colvarbias_meta::read_restart(), colvarbias_harmonic::read_restart(), colvar::read_restart(), colvarmodule::atom::read_velocity(), colvar::rmsd::rmsd(), colvar::selfcoordnum::selfcoordnum(), colvarmodule::atom_group::system_force(), colvarmodule::atom_group::system_forces(), colvarvalue::undef_op(), colvarbias_meta::update(), colvarbias_histogram::update(), colvarbias_meta::update_replicas_registry(), colvar_grid_scalar::value_input(), colvar_grid_scalar::value_output(), colvarmodule::atom_group::velocities(), colvar_grid< size_t >::wrap(), colvar_grid_gradient::write_1D_integral(), colvar::write_output_files(), and colvarbias_meta::write_replica_state_file(). { proxy->fatal_error (message); }

void cvm::increase_depth (   )  [static]

Increase the depth (number of indentations in the output). Definition at line 702 of file colvarmodule.C. References depth. Referenced by analyze(), calc(), colvar::calc(), change_configuration(), colvar::communicate_forces(), energy_difference(), init_biases(), init_colvars(), colvarmodule::atom_group::parse(), read_restart(), colvar::update(), write_output_files(), and write_restart(). { depth++; }

void colvarmodule::init_biases (  std::string const &  conf  )

Initialize collective variable biases. initialize ABF instances initialize harmonic restraints initialize histograms initialize metadynamics instances Definition at line 212 of file colvarmodule.C. References biases, colvarparse::check_keywords(), debug(), decrease_depth(), increase_depth(), colvarparse::key_lookup(), log(), n_abf_biases, n_harm_biases, n_histo_biases, n_meta_biases, and parse. Referenced by colvarmodule(). { if (cvm::debug()) cvm::log ("Initializing the collective variables biases.\n"); { std::string abf_conf = ""; size_t abf_pos = 0; while (parse->key_lookup (conf, "abf", abf_conf, abf_pos)) { if (abf_conf.size()) { cvm::log (cvm::line_marker); cvm::increase_depth(); biases.push_back (new colvarbias_abf (abf_conf, "abf")); (biases.back())->check_keywords (abf_conf, "abf"); cvm::decrease_depth(); n_abf_biases++; } else { cvm::log ("Warning: \"abf\" keyword found without configuration.\n"); } abf_conf = ""; } } { std::string harm_conf = ""; size_t harm_pos = 0; while (parse->key_lookup (conf, "harmonic", harm_conf, harm_pos)) { if (harm_conf.size()) { cvm::log (cvm::line_marker); cvm::increase_depth(); biases.push_back (new colvarbias_harmonic (harm_conf, "harmonic")); (biases.back())->check_keywords (harm_conf, "harmonic"); cvm::decrease_depth(); n_harm_biases++; } else { cvm::log ("Warning: \"harmonic\" keyword found without configuration.\n"); } harm_conf = ""; } } { std::string histo_conf = ""; size_t histo_pos = 0; while (parse->key_lookup (conf, "histogram", histo_conf, histo_pos)) { if (histo_conf.size()) { cvm::log (cvm::line_marker); cvm::increase_depth(); biases.push_back (new colvarbias_histogram (histo_conf, "histogram")); (biases.back())->check_keywords (histo_conf, "histogram"); cvm::decrease_depth(); n_histo_biases++; } else { cvm::log ("Warning: \"histogram\" keyword found without configuration.\n"); } histo_conf = ""; } } { std::string meta_conf = ""; size_t meta_pos = 0; while (parse->key_lookup (conf, "metadynamics", meta_conf, meta_pos)) { if (meta_conf.size()) { cvm::log (cvm::line_marker); cvm::increase_depth(); biases.push_back (new colvarbias_meta (meta_conf, "metadynamics")); (biases.back())->check_keywords (meta_conf, "metadynamics"); cvm::decrease_depth(); n_meta_biases++; } else { cvm::log ("Warning: \"metadynamics\" keyword found without configuration.\n"); } meta_conf = ""; } } if (biases.size()) cvm::log (cvm::line_marker); cvm::log ("Collective variables biases initialized, "+ cvm::to_str (biases.size())+" in total.\n"); }

void colvarmodule::init_colvars (  std::string const &  conf  )

Initialize collective variables. Definition at line 179 of file colvarmodule.C. References colvarparse::check_keywords(), colvars, debug(), decrease_depth(), fatal_error(), increase_depth(), colvarparse::key_lookup(), log(), and parse. Referenced by colvarmodule(). { if (cvm::debug()) cvm::log ("Initializing the collective variables.\n"); std::string colvar_conf = ""; size_t pos = 0; while (parse->key_lookup (conf, "colvar", colvar_conf, pos)) { if (colvar_conf.size()) { cvm::log (cvm::line_marker); cvm::increase_depth(); colvars.push_back (new colvar (colvar_conf)); (colvars.back())->check_keywords (colvar_conf, "colvar"); cvm::decrease_depth(); } else { cvm::log ("Warning: \"colvar\" keyword found without any configuration.\n"); } colvar_conf = ""; } if (!colvars.size()) cvm::fatal_error ("Error: no collective variables defined.\n"); if (colvars.size()) cvm::log (cvm::line_marker); cvm::log ("Collective variables initialized, "+ cvm::to_str (colvars.size())+ " in total.\n"); }

void cvm::load_atoms (  char const *  filename, std::vector< atom > &  atoms, std::string const &  pdb_field, double const   pdb_field_value = 0.0 )  [inline, static]

Create atoms from a file. Parameters: filename  name of the file (usually a PDB) atoms  array of the atoms to be allocated pdb_field  (optiona) if "filename" is a PDB file, use this field to determine which are the atoms to be set Definition at line 462 of file colvarmodule.h. References colvarproxy::load_atoms(), and proxy. Referenced by colvarmodule::atom_group::parse(). { proxy->load_atoms (file_name, atoms, pdb_field, pdb_field_value); }

void cvm::load_coords (  char const *  filename, std::vector< atom_pos > &  pos, const std::vector< int > &  indices, std::string const &  pdb_field, double const   pdb_field_value = 0.0 )  [inline, static]

Load the coordinates for a group of atoms from a file (usually a PDB); the number of atoms in "filename" must match the number of elements in "pos". Definition at line 470 of file colvarmodule.h. References colvarproxy::load_coords(), and proxy. Referenced by colvar::eigenvector::eigenvector(), colvar::orientation::orientation(), colvarmodule::atom_group::parse(), and colvar::rmsd::rmsd(). { proxy->load_coords (file_name, pos, indices, pdb_field, pdb_field_value); }

void cvm::log (  std::string const &  message  )  [static]

Print a message to the main log. Definition at line 694 of file colvarmodule.C. References depth, colvarproxy::log(), and proxy. Referenced by colvarbias::add_colvar(), colvar::alpha_angles::alpha_angles(), analyze(), colvar::angle::angle(), colvarmodule::atom::atom(), colvarmodule::atom_group::atom_group(), colvar::build_atom_list(), calc(), colvar::calc(), colvar::calc_acf(), colvarmodule::atom_group::calc_fit_gradients(), colvar::tilt::calc_gradients(), colvar::eigenvector::calc_gradients(), colvar::rmsd::calc_gradients(), colvar::inertia_z::calc_gradients(), colvar::inertia::calc_gradients(), colvar::gyration::calc_gradients(), colvar::calc_runave(), colvar::alpha_angles::calc_value(), colvarproxy_namd::calculate(), colvarparse::check_keywords(), colvarvalue::check_types(), colvar::colvar(), colvar_grid< size_t >::colvar_grid(), colvarbias::colvarbias(), colvarbias_abf::colvarbias_abf(), colvarbias_harmonic::colvarbias_harmonic(), colvarbias_histogram::colvarbias_histogram(), colvarbias_meta::colvarbias_meta(), colvarmodule(), colvarproxy_namd::colvarproxy_namd(), colvarbias::communicate_forces(), colvar::communicate_forces(), colvar::cvc::cvc(), colvar::cvc::debug_gradients(), colvarbias_meta::delete_hill(), colvar::dihedPC::dihedPC(), colvar::dihedral::dihedral(), colvar::distance::distance(), colvar::distance_z::distance_z(), colvar::eigenvector::eigenvector(), colvar::enable(), colvarproxy_namd::exit(), colvarproxy_namd::fatal_error(), colvar::gyration::gyration(), colvar::h_bond::h_bond(), colvarbias_meta::hill::hill(), colvar::inertia_z::inertia_z(), init_biases(), init_colvars(), colvar_grid< size_t >::map_grid(), colvar::orientation::orientation(), colvarmodule::atom_group::parse(), colvar::parse_analysis(), colvarbias_meta::project_hills(), colvarbias_meta::read_hill(), colvar_grid< size_t >::read_multicol(), colvarbias_meta::read_replica_files(), colvar_grid_gradient::read_restart(), colvar_grid_scalar::read_restart(), colvar_grid_count::read_restart(), colvarbias_meta::read_restart(), colvarbias_harmonic::read_restart(), colvar::read_restart(), read_traj(), colvar::read_traj(), colvar::rmsd::rmsd(), colvar::spin_angle::spin_angle(), colvar::tilt::tilt(), colvarbias_meta::update(), colvarbias_histogram::update(), colvarbias_abf::update(), colvarbias_harmonic::update(), colvar::update(), colvarbias_meta::update_replicas_registry(), colvar::write_acf(), write_output_files(), and colvar::write_output_files(). { if (depth > 0) proxy->log ((std::string (2*depth, ' '))+message); else proxy->log (message); }

cvm::real cvm::position_dist2 (  atom_pos const &  pos1, atom_pos const &  pos2 )  [inline, static]

Get the square distance between two positions (with periodic boundary conditions handled transparently). Note: in the case of periodic boundary conditions, this provides an analytical square distance (while taking the square of position_distance() would produce leads to a cusp) Definition at line 456 of file colvarmodule.h. References atom_pos, colvarproxy::position_dist2(), and proxy. Referenced by colvar::distance_vec::dist2(). { return proxy->position_dist2 (pos1, pos2); }

cvm::rvector cvm::position_distance (  atom_pos const &  pos1, atom_pos const &  pos2 )  [inline, static]

Get the distance between two atomic positions with pbcs handled correctly. Definition at line 450 of file colvarmodule.h. References atom_pos, colvarproxy::position_distance(), and proxy. Referenced by colvar::distance_xy::calc_gradients(), colvar::distance_inv::calc_value(), colvar::distance_dir::calc_value(), colvar::distance_xy::calc_value(), colvar::distance_z::calc_value(), colvar::distance_vec::calc_value(), colvar::distance::calc_value(), colvar::dihedral::calc_value(), colvar::angle::calc_value(), colvar::distance_vec::dist2_lgrad(), colvar::distance_vec::dist2_rgrad(), colvar::selfcoordnum::switching_function(), and colvar::coordnum::switching_function(). { return proxy->position_distance (pos1, pos2); }

cvm::real cvm::rand_gaussian (  void   )  [inline, static]

Pseudo-random number with Gaussian distribution. Definition at line 484 of file colvarmodule.h. References proxy, and colvarproxy::rand_gaussian(). Referenced by colvar::update(). { return proxy->rand_gaussian(); }

std::istream & colvarmodule::read_restart (  std::istream &  is  )

Read the input restart file. Definition at line 138 of file colvarmodule.C. References biases, colvars, decrease_depth(), fatal_error(), increase_depth(), it, it_restart, and parse. Referenced by colvarmodule(). { { // read global restart information std::string restart_conf; if (is >> colvarparse::read_block ("configuration", restart_conf)) { if (it_restart_from_state_file) { parse->get_keyval (restart_conf, "step", it_restart, (size_t) 0, colvarparse::parse_silent); it = it_restart; } } is.clear(); } // colvars restart cvm::increase_depth(); for (std::vector<colvar *>::iterator cvi = colvars.begin(); cvi != colvars.end(); cvi++) { if ( !((*cvi)->read_restart (is)) ) cvm::fatal_error ("Error: in reading restart configuration for collective variable \""+ (*cvi)->name+"\".\n"); } // biases restart for (std::vector<colvarbias *>::iterator bi = biases.begin(); bi != biases.end(); bi++) { if (!((*bi)->read_restart (is))) fatal_error ("Error: in reading restart configuration for bias \""+ (*bi)->name+"\".\n"); } cvm::decrease_depth(); return is; }

bool colvarmodule::read_traj (  char const *  traj_filename, size_t  traj_read_begin, size_t  traj_read_end )

Read a collective variable trajectory (post-processing only, not called at runtime). Definition at line 599 of file colvarmodule.C. References colvars, colvarparse::getline_nocomments(), it, and log(). { cvm::log ("Opening trajectory file \""+ std::string (traj_filename)+"\".\n"); std::ifstream traj_is (traj_filename); while (true) { while (true) { std::string line (""); do { if (!colvarparse::getline_nocomments (traj_is, line)) { cvm::log ("End of file \""+std::string (traj_filename)+ "\" reached, or corrupted file.\n"); traj_is.close(); return false; } } while (line.find_first_not_of (colvarparse::white_space) == std::string::npos); std::istringstream is (line); if (!(is >> it)) return false; if ( (it < traj_read_begin) ) { if ((it % 1000) == 0) std::cerr << "Skipping trajectory step " << it << " \r"; continue; } else { if ((it % 1000) == 0) std::cerr << "Reading from trajectory, step = " << it << " \r"; if ( (traj_read_end > traj_read_begin) && (it > traj_read_end) ) { std::cerr << "\n"; cvm::log ("Reached the end of the trajectory, " "read_end = "+cvm::to_str (traj_read_end)+"\n"); return false; } for (std::vector<colvar *>::iterator cvi = colvars.begin(); cvi != colvars.end(); cvi++) { if (!(*cvi)->read_traj (is)) { cvm::log ("Error: in reading colvar \""+(*cvi)->name+ "\" from trajectory file \""+ std::string (traj_filename)+"\".\n"); return false; } } break; } } } return true; }

void cvm::request_system_force (   )  [inline, static]

Request calculation of system force from MD engine. Definition at line 433 of file colvarmodule.h. References proxy, and colvarproxy::request_system_force(). Referenced by colvar::enable(). { proxy->request_system_force (true); }

void cvm::select_closest_image (  atom_pos &  pos, atom_pos const &  ref_pos )  [inline, static]

Get the closest periodic image to a reference position. Parameters: pos  The position to look for the closest periodic image ref_pos  (optional) The reference position Definition at line 438 of file colvarmodule.h. References atom_pos, proxy, and colvarproxy::select_closest_image(). { proxy->select_closest_image (pos, ref_pos); }

void cvm::select_closest_images (  std::vector< atom_pos > &  pos, atom_pos const &  ref_pos )  [inline, static]

Perform select_closest_image() on a set of atomic positions. After that, distance vectors can then be calculated directly, without using position_distance() Definition at line 444 of file colvarmodule.h. References atom_pos, proxy, and colvarproxy::select_closest_images(). { proxy->select_closest_images (pos, ref_pos); }

size_t colvarmodule::step_absolute (   )  [inline, static]

Return the current step number from the beginning of the whole calculation Definition at line 100 of file colvarmodule.h. Referenced by calc(), colvarbias_meta::update(), colvarbias_histogram::update(), colvarbias_abf::update(), colvarbias_harmonic::update(), colvarbias_meta::write_replica_state_file(), and colvarbias_meta::write_restart(). { return it; }

size_t colvarmodule::step_relative (   )  [inline, static]

Return the current step number from the beginning of this run. Definition at line 93 of file colvarmodule.h. Referenced by analyze(), calc(), colvar::calc(), colvar::calc_runave(), colvarproxy_namd::calculate(), colvarbias_abf::update(), and colvarbias_harmonic::update(). { return it - it_restart; }

cvm::real cvm::temperature (   )  [inline, static]

Temperature of the simulation (K). Definition at line 423 of file colvarmodule.h. References proxy, and colvarproxy::temperature(). Referenced by colvarbias_abf::colvarbias_abf(), colvar::update(), and colvarbias_meta::write_pmf(). { return proxy->temperature(); }

template<typename T> std::string cvm::to_str (  std::vector< T > const &  x, size_t const &  width = 0, size_t const &  prec = 0 )  [static]

Quick conversion of a vector of objects to a string. Definition at line 387 of file colvarmodule.h. { if (!x.size()) return std::string (""); std::ostringstream os; if (prec) { os.setf (std::ios::scientific, std::ios::floatfield); } os << "{ "; if (width) os.width (width); if (prec) os.precision (prec); os << x[0]; for (size_t i = 1; i < x.size(); i++) { os << ", "; if (width) os.width (width); if (prec) os.precision (prec); os << x[i]; } os << " }"; return os.str(); }

template<typename T> std::string cvm::to_str (  T const &  x, size_t const &  width = 0, size_t const &  prec = 0 )  [static]

Quick conversion of an object to a string. Definition at line 374 of file colvarmodule.h. Referenced by colvar::alpha_angles::calc_value(), colvarmodule::atom_group::create_sorted_ids(), colvar::dihedPC::dihedPC(), colvarbias_meta::hill::hill(), colvarmodule::atom_group::parse(), and colvar::rmsd::rmsd(). { std::ostringstream os; if (width) os.width (width); if (prec) { os.setf (std::ios::scientific, std::ios::floatfield); os.precision (prec); } os << x; return os.str(); }

cvm::real cvm::unit_angstrom (   )  [inline, static]

Value of the unit for atomic coordinates with respect to angstroms (used by some variables for hard-coded default values). Definition at line 413 of file colvarmodule.h. References proxy, and colvarproxy::unit_angstrom(). { return proxy->unit_angstrom(); }

std::string colvarmodule::wrap_string (  std::string const &  s, size_t const &  nchars )  [inline, static]

Reduce the number of characters in a string. Definition at line 211 of file colvarmodule.h. Referenced by calc(), colvar::parse_analysis(), and colvar::write_traj_label(). { if (!s.size()) return std::string (nchars, ' '); else return ( (s.size() <= size_t (nchars)) ? (s+std::string (nchars-s.size(), ' ')) : (std::string (s, 0, nchars)) ); }

void colvarmodule::write_output_files (   )

Write all output files (called by the proxy). Definition at line 570 of file colvarmodule.C. References colvarproxy::backup_file(), colvars, cv_traj_os, decrease_depth(), increase_depth(), log(), output_prefix, proxy, and write_restart(). Referenced by colvarproxy_namd::calculate(). { // if this is a simulation run (i.e. not a postprocessing), output data // must be written to be able to restart the simulation std::string const out_name = (output_prefix.size() ? std::string (output_prefix+".colvars.state") : std::string ("colvars.state")); cvm::log ("Saving collective variables state to \""+out_name+"\".\n"); proxy->backup_file (out_name.c_str()); std::ofstream out (out_name.c_str()); out.setf (std::ios::scientific, std::ios::floatfield); this->write_restart (out); out.close(); cvm::increase_depth(); for (std::vector<colvar *>::iterator cvi = colvars.begin(); cvi != colvars.end(); cvi++) { (*cvi)->write_output_files(); } cvm::decrease_depth(); // do not close to avoid problems with multiple NAMD runs cv_traj_os.flush(); }

std::ostream & colvarmodule::write_restart (  std::ostream &  os  )

Write the output restart file. Definition at line 667 of file colvarmodule.C. References biases, colvars, decrease_depth(), dt(), increase_depth(), it, and it_width. Referenced by calc(), and write_output_files(). { os << "configuration {\n" << " step " << std::setw (it_width) << it << "\n" << " dt " << dt() << "\n" << "}\n\n"; cvm::increase_depth(); for (std::vector<colvar *>::iterator cvi = colvars.begin(); cvi != colvars.end(); cvi++) { (*cvi)->write_restart (os); } for (std::vector<colvarbias *>::iterator bi = biases.begin(); bi != biases.end(); bi++) { (*bi)->write_restart (os); } cvm::decrease_depth(); return os; }

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Friends And Related Function Documentation

friend class atom [friend]

Definition at line 82 of file colvarmodule.h. Referenced by colvar::h_bond::h_bond().

friend class atom_group [friend]

Definition at line 83 of file colvarmodule.h.

friend class colvarproxy [friend]

Definition at line 56 of file colvarmodule.h.

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Member Data Documentation

bool colvarmodule::b_analysis = false [static]

True if only analysis is performed and not a run. Definition at line 741 of file colvarmodule.C. Referenced by colvarmodule().

std::vector< colvarbias * > colvarmodule::biases [static]

Array of collective variable biases. Definition at line 726 of file colvarmodule.C. Referenced by analyze(), calc(), change_configuration(), energy_difference(), init_biases(), read_restart(), write_restart(), and ~colvarmodule().

std::vector< colvar * > colvarmodule::colvars [static]

Array of collective variables. Definition at line 725 of file colvarmodule.C. Referenced by analyze(), calc(), init_colvars(), read_restart(), read_traj(), write_output_files(), write_restart(), and ~colvarmodule().

std::ifstream colvarmodule::config_s [protected]

Configuration file. Definition at line 328 of file colvarmodule.h. Referenced by colvarmodule().

size_t const colvarmodule::cv_prec = 14 [static]

Number of digits to represent a collective variables value(s). Definition at line 753 of file colvarmodule.C.

bool colvarmodule::cv_traj_append [protected]

Appending to the existing trajectory file? Definition at line 340 of file colvarmodule.h. Referenced by colvarmodule().

size_t colvarmodule::cv_traj_freq = 0 [static]

Frequency for collective variables trajectory output. Definition at line 739 of file colvarmodule.C. Referenced by calc(), and colvarmodule().

std::string colvarmodule::cv_traj_name [protected]

Name of the trajectory file. Definition at line 334 of file colvarmodule.h. Referenced by calc(), and colvarmodule().

std::ofstream colvarmodule::cv_traj_os [protected]

Collective variables output trajectory file. Definition at line 337 of file colvarmodule.h. Referenced by calc(), colvarmodule(), write_output_files(), and ~colvarmodule().

size_t const colvarmodule::cv_width = 21 [static]

Number of characters to represent a collective variables value(s). Definition at line 754 of file colvarmodule.C.

cvm::real colvarmodule::debug_gradients_step_size = 1.0e-03 [static]

Finite difference step size (if there is no dynamics, or if gradients need to be tested independently from the size of dt). Definition at line 735 of file colvarmodule.C. Referenced by colvarmodule().

size_t colvarmodule::depth = 0 [static, protected]

Counter for the current depth in the object hierarchy (useg e.g. in outpu. Definition at line 740 of file colvarmodule.C. Referenced by decrease_depth(), increase_depth(), and log().

size_t const colvarmodule::en_prec = 14 [static]

Number of digits to represent the collective variables energy. Definition at line 755 of file colvarmodule.C.

size_t const colvarmodule::en_width = 21 [static]

Number of characters to represent the collective variables energy. Definition at line 756 of file colvarmodule.C.

std::string colvarmodule::input_prefix = "" [static]

Prefix for files from a previous run (including restart/output). Definition at line 747 of file colvarmodule.C.

size_t colvarmodule::it = 0 [static]

Current step number. Definition at line 736 of file colvarmodule.C. Referenced by analyze(), calc(), colvarproxy_namd::calculate(), colvarmodule(), colvarproxy_namd::colvarproxy_namd(), read_restart(), read_traj(), and write_restart().

size_t colvarmodule::it_restart = 0 [static]

Starting step number for this run. Definition at line 737 of file colvarmodule.C. Referenced by colvarmodule(), colvarproxy_namd::colvarproxy_namd(), and read_restart().

bool colvarmodule::it_restart_from_state_file

If true, get it_restart from the state file; if set to false, the MD program is providing it Definition at line 107 of file colvarmodule.h. Referenced by colvarmodule().

size_t const colvarmodule::it_width = 12 [static]

Number of characters to represent a time step. Definition at line 752 of file colvarmodule.C. Referenced by write_restart().

std::string const colvarmodule::line_marker [static]

Initial value: "----------------------------------------------------------------------\n" Line separator in the log output. Definition at line 757 of file colvarmodule.C.

size_t colvarmodule::n_abf_biases = 0 [static]

Number of ABF biases initialized (in normal conditions should be 1). Definition at line 727 of file colvarmodule.C. Referenced by init_biases().

size_t colvarmodule::n_harm_biases = 0 [static]

Number of harmonic biases initialized (no limit on the number). Definition at line 728 of file colvarmodule.C. Referenced by init_biases().

size_t colvarmodule::n_histo_biases = 0 [static]

Number of histograms initialized (no limit on the number). Definition at line 729 of file colvarmodule.C. Referenced by init_biases().

size_t colvarmodule::n_meta_biases = 0 [static]

Number of metadynamics biases initialized (in normal conditions should be 1). Definition at line 730 of file colvarmodule.C. Referenced by init_biases().

std::string colvarmodule::output_prefix = "" [static]

Prefix for all output files for this run. Definition at line 746 of file colvarmodule.C. Referenced by colvarmodule(), and write_output_files().

colvarparse* colvarmodule::parse [protected]

Configuration file parser object. Definition at line 331 of file colvarmodule.h. Referenced by colvarmodule(), init_biases(), init_colvars(), and read_restart().

colvarproxy * colvarmodule::proxy = NULL [static, protected]

Pointer to the proxy object, used to retrieve atomic data from the hosting program; it is static in order to be accessible from static functions in the colvarmodule class. Definition at line 731 of file colvarmodule.C. Referenced by backup_file(), boltzmann(), calc(), colvarmodule(), dt(), exit(), fatal_error(), load_atoms(), load_coords(), log(), position_dist2(), position_distance(), rand_gaussian(), request_system_force(), select_closest_image(), select_closest_images(), temperature(), unit_angstrom(), and write_output_files().

std::string colvarmodule::restart_in_name = "" [static]

input restart file name (determined from input_prefix) Definition at line 748 of file colvarmodule.C. Referenced by colvarmodule().

size_t colvarmodule::restart_out_freq = 0 [static]

Frequency for saving output restarts. Definition at line 738 of file colvarmodule.C. Referenced by calc(), and colvarmodule().

std::string colvarmodule::restart_out_name

Output restart file name. Definition at line 321 of file colvarmodule.h. Referenced by calc(), and colvarmodule().

std::ofstream colvarmodule::restart_out_os [protected]

Output restart file. Definition at line 343 of file colvarmodule.h. Referenced by calc().

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

• colvarmodule.h
• colvar.h
• colvarmodule.C

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