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colvarmodule.h File Reference

#include <cmath>
#include "colvars_version.h"
#include <sstream>
#include <string>
#include <vector>
#include <list>
#include <iosfwd>

Go to the source code of this file.

Compounds
class	colvarmodule
	\brief 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. More...
Defines
#define	COLVARS_DEBUG   false
#define	COLVARS_OK   0
	\file colvarmodule.h \brief Collective variables main module This file declares the main class for defining and manipulating collective variables: there should be only one instance of this class, because several variables are made static (i.e. they are shared between all object instances) to be accessed from other objects. More...
#define	COLVARS_ERROR   1
#define	COLVARS_NOT_IMPLEMENTED   (1<<1)
#define	COLVARS_INPUT_ERROR   (1<<2)
#define	COLVARS_BUG_ERROR   (1<<3)
#define	COLVARS_FILE_ERROR   (1<<4)
#define	COLVARS_MEMORY_ERROR   (1<<5)
#define	COLVARS_NO_SUCH_FRAME   (1<<6)
Typedefs
typedef colvarmodule	cvm
	Shorthand for the frequently used type prefix. More...
Functions
std::ostream &	operator<< (std::ostream &os, cvm::rvector const &v)
std::istream &	operator>> (std::istream &is, cvm::rvector &v)

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Define Documentation

#define COLVARS_BUG_ERROR   (1<<3)

Definition at line 40 of file colvarmodule.h. Referenced by colvarparse::_get_keyval_vector_, colvar_grid< size_t >::address, colvar::check_cvc_range, colvardeps::check_enabled, colvarproxy_io::close_output_stream, colvarmodule::colvarmodule, colvarproxy_io::input_stream, colvarvalue::interpolate, colvarproxy_vmd::load_coords, colvarvalue::operator[], colvarproxy_io::output_stream, colvarproxy::parse_module_config, colvarbias_meta::project_hills, colvarbias::read_state_string, colvarmodule::matrix2d::row::set, colvar_grid< size_t >::setup, colvarbias_meta::setup_output, colvarproxy_vmd::update_atomic_properties, colvarproxy_system::update_pbc_lattice, and colvar_grid< size_t >::wrap.

#define COLVARS_DEBUG   false

Definition at line 18 of file colvarmodule.h. Referenced by colvarmodule::debug.

#define COLVARS_ERROR   1

Definition at line 37 of file colvarmodule.h. Referenced by colvarmodule::analyze, colvarproxy_io::backup_file, colvarmodule::calc_biases, colvarmodule::calc_colvars, colvarmodule::calc_scripted_forces, colvarmodule::change_configuration, colvarvalue::check_types, colvarvalue::check_types_assign, colvardeps::decr_ref_count, colvardeps::disable, colvardeps::enable, colvarmodule::end_of_step, colvarvalue::from_simple_string, colvarmodule::matrix2d::from_simple_string, colvarmodule::vector1d::from_simple_string, colvarbias_restraint_k_moving::init, colvarbias_abf::init, colvar::init, colvar_grid< size_t >::init_from_colvars, colvar::cvc::init_total_force_params, colvarproxy_vmd::load_atoms, colvarproxy_vmd::load_coords, colvar::parse_analysis, colvarmodule::parse_biases, colvarmodule::parse_colvars, colvar_grid< size_t >::parse_params, colvarmodule::read_traj, colvarmodule::reset, colvar::set_cvc_flags, colvarmodule::set_error_bits, colvarproxy_vmd::set_unit_system, colvarproxy_vmd::setup, colvar_grid< size_t >::setup, colvarproxy_smp::smp_enabled, colvarproxy_smp::smp_trylock, colvarproxy_tcl::tcl_run_colvar_callback, colvarproxy_tcl::tcl_run_colvar_gradient_callback, colvarproxy_tcl::tcl_run_file, colvarproxy_tcl::tcl_run_force_callback, colvarproxy_tcl::tcl_run_script, colvarmodule::update_colvar_forces, colvar::update_cvc_flags, colvarmodule::update_engine_parameters, colvarproxy_vmd::update_input, and colvarmodule::write_restart_file.

#define COLVARS_FILE_ERROR   (1<<4)

Definition at line 41 of file colvarmodule.h. Referenced by colvarproxy_io::close_input_stream, colvarbias_restraint_histogram::init, colvarproxy_io::input_stream, colvarproxy_vmd::load_atoms, colvarproxy_vmd::load_coords, colvarproxy_io::output_stream, colvarmodule::read_config_file, colvar_grid::read_multicol, colvarbias::read_state_prefix, colvarbias::read_state_string, colvarmodule::read_traj, colvarproxy_io::remove_file, colvarproxy_io::rename_file, colvarbias_meta::reopen_replica_buffer_file, colvarmodule::setup_input, colvarmodule::setup_output, colvarbias_meta::setup_output, colvarbias_meta::update_bias, colvarbias_meta::update_replicas_registry, colvar::write_acf, colvarbias_reweightaMD::write_count, colvarbias_reweightaMD::write_cumulant_expansion_pmf, colvarbias_reweightaMD::write_exponential_reweighted_pmf, colvar_grid::write_multicol, colvar_grid::write_opendx, colvarbias_ti::write_output_files, colvar::write_output_files, colvarbias_meta::write_replica_state_file, colvarmodule::write_restart_file, colvarmodule::write_restart_string, colvarbias::write_state_prefix, colvarbias::write_state_string, and colvarmodule::write_traj_files.

#define COLVARS_INPUT_ERROR   (1<<2)

Definition at line 39 of file colvarmodule.h. Referenced by colvarparse::_get_keyval_scalar_novalue_, colvarparse::_get_keyval_scalar_value_, colvarparse::_get_keyval_vector_, colvarbias::add_colvar, colvar::calc_acf, colvarproxy_vmd::check_atom_id, colvarparse::check_braces, colvarparse::check_keywords, colvarproxy_vmd::check_volmap_by_id, colvarproxy_atoms::clear_atom, colvarproxy_atom_groups::clear_atom_group, colvarproxy_volmaps::clear_volmap, colvar::collect_cvc_values, colvar_grid_gradient::colvar_grid_gradient, colvar::coordnum::coordnum, colvarparse::error_key_required, colvarparse::get_key_string_value, colvarparams::get_param_grad_ptr, colvarparams::get_param_ptr, colvar::map_total::init, colvar::orientation::init, colvar::cvc::init, colvarbias_restraint_histogram::init, colvarbias_restraint_linear::init, colvarbias_restraint_harmonic_walls::init, colvarbias_restraint_k_moving::init, colvarbias_restraint_centers_moving::init, colvarbias_restraint_moving::init, colvarbias_restraint_k::init, colvarbias_restraint_centers::init, colvarbias_meta::init, colvarbias_reweightaMD::init, colvarbias_histogram::init, colvarbias_abf::init, colvarbias_ti::init, colvarbias::init, colvar::init, colvarproxy_vmd::init_atom, colvar::init_components, colvarbias_meta::init_ebmeta_params, colvar::init_extended_Lagrangian, colvar_grid< size_t >::init_from_colvars, colvar::init_grid_parameters, colvar::init_output_flags, colvarbias_meta::init_replicas_params, colvarbias_meta::init_well_tempered_params, colvarvalue::interpolate, colvarparse::key_lookup, colvarproxy_vmd::load_atoms, colvarproxy_vmd::load_coords, colvarparams::param_exists, colvar::parse_analysis, colvarmodule::parse_colvars, colvarmodule::parse_config, colvar::cvc::parse_group, colvarproxy_system::position_distance, colvarmodule::print_total_forces_errning, colvarbias_meta::read_hill, colvar_grid::read_multicol, colvarmodule::read_objects_state, colvarmodule::read_restart, colvarbias::read_state, colvar::read_state, colvarbias::read_state_data_key, colvarparams::set_param, colvarbias_meta::set_state_params, colvarbias::set_state_params, simple_scalar_dist_functions, colvarmodule::state_file_prefix, and colvar::update_cvc_config.

#define COLVARS_MEMORY_ERROR   (1<<5)

Definition at line 42 of file colvarmodule.h.

#define COLVARS_NO_SUCH_FRAME   (1<<6)

Definition at line 43 of file colvarmodule.h. Referenced by colvarproxy_vmd::set_frame, and colvarproxy_vmd::update_input.

#define COLVARS_NOT_IMPLEMENTED   (1<<1)

Definition at line 38 of file colvarmodule.h. Referenced by colvarproxy_system::apply_force_dE_dlambda, colvarbias::bin_count, colvarbias::bin_num, colvar::cvc::calc_force_invgrads, colvar::cvc::calc_Jacobian_derivative, colvarmodule::calc_scripted_forces, colvarbias_restraint_k_moving::change_configuration, colvarbias_restraint_centers_moving::change_configuration, colvarbias_restraint_moving::change_configuration, colvarbias_restraint::change_configuration, colvarbias::change_configuration, colvarproxy_atoms::check_atom_id, colvarproxy_volmaps::check_volmap_by_id, colvar::collect_cvc_values, colvar::communicate_forces, colvarproxy_volmaps::compute_volmap, colvarbias::current_bin, colvar::cvc_param_exists, colvarbias::energy_difference, colvarproxy_system::get_accelMD_factor, colvarproxy_system::get_alch_lambda, colvarproxy_atom_groups::get_atom_group_velocity, colvarproxy_atoms::get_atom_velocity, colvar::get_cvc_param, colvar::get_cvc_param_grad, colvar::get_cvc_param_ptr, colvarproxy_system::get_d2E_dlambda2, colvarproxy_system::get_dE_dlambda, colvarproxy_io::get_frame, colvarproxy_system::get_molid, colvarbias_abf::init, colvarbias_ti::init, colvarproxy_atoms::init_atom, colvarproxy_atom_groups::init_atom_group, colvar::init_custom_function, colvarproxy_atoms::load_atoms, colvarproxy_atoms::load_coords, colvarproxy_replicas::replica_comm_recv, colvarproxy_replicas::replica_comm_send, colvarproxy_replicas::replica_enabled, colvarbias::replica_share, colvarproxy::request_deletion, colvarproxy_system::request_total_force, colvarproxy_script::run_colvar_callback, colvarproxy_script::run_colvar_gradient_callback, colvarproxy_script::run_force_callback, colvarproxy_atom_groups::scalable_group_coms, colvarproxy_system::send_alch_lambda, colvar::set_cvc_param, colvarproxy_io::set_frame, colvarparams::set_param, colvarproxy_system::set_unit_system, colvarproxy_smp::smp_biases_loop, colvarproxy_smp::smp_biases_script_loop, colvarproxy_smp::smp_colvars_loop, colvarproxy_smp::smp_enabled, colvarproxy_tcl::tcl_run_colvar_callback, colvarproxy_tcl::tcl_run_colvar_gradient_callback, colvarproxy_tcl::tcl_run_file, colvarproxy_tcl::tcl_run_force_callback, colvarproxy_tcl::tcl_run_script, colvarbias_restraint_histogram::update, and colvarproxy_volmaps::volmaps_available.

return COLVARS_OK   0

\file colvarmodule.h \brief Collective variables main module This file declares the main class for defining and manipulating collective variables: there should be only one instance of this class, because several variables are made static (i.e. they are shared between all object instances) to be accessed from other objects. Definition at line 36 of file colvarmodule.h.

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Typedef Documentation

typedef colvarmodule cvm

Shorthand for the frequently used type prefix. Definition at line 837 of file colvarmodule.h.

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Function Documentation

std::ostream& operator<< (  std::ostream &    os, cvm::rvector const &    v )

std::istream& operator>> (  std::istream &    is, cvm::rvector &    v )

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