colvarbias class Reference

Public Methods

int add_colvar (std::string const &cv_name)

Add a new collective variable to this bias. More...

size_t num_variables () const

How many variables are defined for this bias. More...

std::vector< colvar * > * variables ()

Access the variables vector. More...

colvar * variables (int i) const

Access the i-th variable. More...

virtual int update ()

Retrieve colvar values and calculate their biasing forces Some implementations may use calc_energy() and calc_forces(). More...

virtual bool can_accumulate_data ()

Returns true if the current step represent a valid increment, whose data can be recorded (as opposed to e.g. a continuation step from a restart). More...

virtual int calc_energy (std::vector< colvarvalue > const *values)

Compute the energy of the bias Uses the vector of colvar values provided if not NULL, and the values currently cached in the bias instance otherwise. More...

virtual int calc_forces (std::vector< colvarvalue > const *values)

Compute the forces due to the bias Uses the vector of colvar values provided if not NULL, and the values currently cached in the bias instance otherwise. More...

int communicate_forces ()

Send forces to the collective variables. More...

virtual int end_of_step ()

Carry out operations needed before next step is run. More...

virtual int change_configuration (std::string const &conf)

Load new configuration - force constant and/or centers only. More...

virtual cvm::real energy_difference (std::string const &conf)

Calculate change in energy from using alternate configuration. More...

virtual int bin_num ()

Give the total number of bins for a given bias. More...

virtual int current_bin ()

Calculate the bin index for a given bias. More...

virtual int bin_count (int bin_index)

virtual int replica_share ()

virtual void analyze ()

Perform analysis tasks. More...

colvarbias (char const *key)

\brief Constructor. More...

virtual int init (std::string const &conf)

\brief Parse config string and (re)initialize. More...

virtual int init_dependencies ()

\brief Initialize dependency tree. More...

virtual int reset ()

\brief Set to zero all mutable data. More...

virtual int clear ()

\brief Delete everything. More...

virtual int clear_state_data ()

\brief Delete only the allocatable data (save memory). More...

virtual ~colvarbias ()

Destructor. More...

virtual std::string const get_state_params () const

Write the values of specific mutable properties to a string. More...

virtual int set_state_params (std::string const &state_conf)

Read the values of specific mutable properties from a string. More...

virtual std::ostream & write_state_data (std::ostream &os)

Write all mutable data not already written by get_state_params(). More...

virtual std::istream & read_state_data (std::istream &is)

Read all mutable data not already set by set_state_params(). More...

std::istream & read_state_data_key (std::istream &is, char const *key)

Read a keyword from the state data (typically a header)
Parameters:

Input stream

Keyword labeling the header block.

More...

std::ostream & write_state (std::ostream &os)

Write the bias configuration to a state file or other stream. More...

std::istream & read_state (std::istream &is)

Read the bias configuration from a restart file or other stream. More...

int write_state_prefix (std::string const &prefix)

Write the bias state to a file with the given prefix. More...

int write_state_string (std::string &output)

Write the bias state to a string. More...

int read_state_prefix (std::string const &prefix)

Read the bias state from a file with this name or prefix. More...

int read_state_string (char const *buffer)

Read the bias state from this string buffer. More...

virtual std::ostream & write_traj_label (std::ostream &os)

Write a label to the trajectory file (comment line). More...

virtual std::ostream & write_traj (std::ostream &os)

Output quantities such as the bias energy to the trajectory file. More...

virtual int setup_output ()

(Re)initialize the output files (does not write them yet). More...

virtual int write_output_files ()

Write any output files that this bias may have (e.g. PMF files). More...

virtual int write_state_to_replicas ()

If this bias is communicating with other replicas through files, send it to them. More...

cvm::real get_energy ()

virtual const std::vector<
feature * > & features () const

\brief Implementation of the feature list accessor for colvarbias. More...

virtual std::vector< feature * > & modify_features ()

Static Public Methods

void delete_features ()

Public Attributes

std::string name

Name of this bias. More...

std::string bias_type

Keyword indicating the type of this bias. More...

std::string state_keyword

Keyword used in state files (== bias_type most of the time). More...

int rank

Track how many times a bias of this type was defined. More...

size_t output_freq

Frequency for writing output files. More...

std::string output_prefix

Use this prefix for all output files. More...

Static Public Attributes

std::vector< feature * > cvb_features

\brief Implementation of the feature list for colvarbias. More...

Protected Attributes

std::vector< colvar * > colvars

\brief Pointers to collective variables to which the bias is applied; current values and metric functions will be obtained through each colvar object. More...

std::vector< colvarvalue > colvar_values

\brief Up to date value of each colvar. More...

std::vector< colvarvalue > colvar_forces

\brief Current forces from this bias to the variables. More...

std::vector< colvarvalue > previous_colvar_forces

\brief Forces last applied by this bias to the variables. More...

cvm::real bias_energy

\brief Current energy of this bias (colvar_forces should be obtained by deriving this). More...

bool b_output_energy

Whether to write the current bias energy from this bias to the trajectory file. More...

bool has_data

\brief Whether this bias has already accumulated information (for history-dependent biases). More...

cvm::step_number state_file_step

\brief Step number read from the last state file. More...

bool matching_state

Flag used to tell if the state string being read is for this bias. More...

colvar_grid_scalar * biasing_force_scaling_factors

\brief The biasing forces will be scaled by the factor in this grid if b_bias_force_scaled is true. More...

std::vector< int > biasing_force_scaling_factors_bin

colvarbias::colvarbias ( char const * key )

\brief Constructor.

Definition at line 20 of file colvarbias.C.

References b_output_energy, bias_type, biasing_force_scaling_factors, colvardeps::description, has_data, init_dependencies, matching_state, NULL, output_freq, rank, reset, state_file_step, state_keyword, colvardeps::time_step_factor, and colvarparse::to_lower_cppstr.

colvarbias::~colvarbias ( ) [virtual]

Destructor.

Definition at line 239 of file colvarbias.C.

References clear.

int colvarbias::add_colvar ( std::string const & cv_name )

Add a new collective variable to this bias.

Definition at line 293 of file colvarbias.C.

References colvardeps::add_child, colvar::biases, colvarmodule::colvar_by_name, colvar_forces, colvars, COLVARS_INPUT_ERROR, colvarmodule::debug, colvarmodule::error, colvarmodule::log, colvar::name, previous_colvar_forces, and colvar::value.

Referenced by init.

virtual void colvarbias::analyze ( void ) [inline, virtual]

Perform analysis tasks.

Definition at line 100 of file colvarbias.h.

int colvarbias::bin_count ( int bin_index ) [virtual]

Definition at line 444 of file colvarbias.C.

References COLVARS_NOT_IMPLEMENTED, and colvarmodule::error.

int colvarbias::bin_num ( ) [virtual]

Give the total number of bins for a given bias.

Definition at line 434 of file colvarbias.C.

References COLVARS_NOT_IMPLEMENTED, and colvarmodule::error.

int colvarbias::calc_energy ( std::vector< colvarvalue > const * values ) [virtual]

Compute the energy of the bias Uses the vector of colvar values provided if not NULL, and the values currently cached in the bias instance otherwise.

Definition at line 358 of file colvarbias.C.

References bias_energy.

Referenced by colvarbias_abf::update, and update.

int colvarbias::calc_forces ( std::vector< colvarvalue > const * values ) [virtual]

Compute the forces due to the bias Uses the vector of colvar values provided if not NULL, and the values currently cached in the bias instance otherwise.

Reimplemented in colvarbias_meta.

Definition at line 365 of file colvarbias.C.

References colvar_forces, and num_variables.

Referenced by update.

bool colvarbias::can_accumulate_data ( ) [virtual]

Returns true if the current step represent a valid increment, whose data can be recorded (as opposed to e.g. a continuation step from a restart).

Definition at line 347 of file colvarbias.C.

References colvardeps::f_cvb_step_zero_data, colvardeps::is_enabled, colvarmodule::main, colvarmodule::proxy, colvarproxy::simulation_continuing, and colvarmodule::step_relative.

Referenced by colvarbias_histogram::update, and colvarbias_meta::update_bias.

int colvarbias::change_configuration ( std::string const & conf ) [virtual]

Load new configuration - force constant and/or centers only.

Reimplemented in colvarbias_restraint.

Definition at line 417 of file colvarbias.C.

References COLVARS_NOT_IMPLEMENTED, and colvarmodule::error.

Referenced by colvarmodule::change_configuration.

int colvarbias::clear ( ) [virtual]

\brief Delete everything.

Reimplemented from colvarparse.

Definition at line 245 of file colvarbias.C.

References colvarmodule::biases, biasing_force_scaling_factors, biasing_force_scaling_factors_bin, colvars, colvarmodule::config_changed, colvardeps::free_children_deps, colvarmodule::main, and NULL.

Referenced by ~colvarbias.

int colvarbias::clear_state_data ( ) [virtual]

\brief Delete only the allocatable data (save memory).

Reimplemented in colvarbias_ti.

Definition at line 286 of file colvarbias.C.

int colvarbias::communicate_forces ( )

Send forces to the collective variables.

Definition at line 374 of file colvarbias.C.

References biasing_force_scaling_factors, biasing_force_scaling_factors_bin, colvar_forces, colvar_grid< cvm::real >::current_bin_scalar, colvarmodule::debug, colvardeps::f_cvb_apply_force, colvardeps::f_cvb_bypass_ext_lagrangian, colvardeps::f_cvb_scale_biasing_force, colvar_grid< cvm::real >::index_ok, colvardeps::is_enabled, colvarmodule::log, num_variables, previous_colvar_forces, colvardeps::time_step_factor, colvar_grid< cvm::real >::value, and variables.

int colvarbias::current_bin ( ) [virtual]

Calculate the bin index for a given bias.

Definition at line 439 of file colvarbias.C.

References COLVARS_NOT_IMPLEMENTED, and colvarmodule::error.

void colvarbias::delete_features ( ) [inline, static]

Definition at line 221 of file colvarbias.h.

References cvb_features.

Referenced by colvarmodule::~colvarmodule.

int colvarbias::end_of_step ( ) [virtual]

Carry out operations needed before next step is run.

Definition at line 411 of file colvarbias.C.

cvm::real colvarbias::energy_difference ( std::string const & conf ) [virtual]

Calculate change in energy from using alternate configuration.

Reimplemented in colvarbias_restraint.

Definition at line 425 of file colvarbias.C.

References COLVARS_NOT_IMPLEMENTED, and colvarmodule::error.

Referenced by colvarmodule::energy_difference.

virtual const std::vector<feature *>& colvarbias::features ( ) const [inline, virtual]

\brief Implementation of the feature list accessor for colvarbias.

Implements colvardeps.

Definition at line 213 of file colvarbias.h.

References cvb_features.

Referenced by init_dependencies.

cvm::real colvarbias::get_energy ( ) [inline]

Definition at line 204 of file colvarbias.h.

References bias_energy.

std::string const colvarbias::get_state_params ( ) const [virtual]

Write the values of specific mutable properties to a string.

Reimplemented in colvarbias_ti.

Definition at line 456 of file colvarbias.C.

References name, and colvarmodule::step_absolute.

Referenced by colvarbias_restraint::get_state_params, colvarbias_meta::get_state_params, and write_state.

int colvarbias::init ( std::string const & conf ) [virtual]

\brief Parse config string and (re)initialize.

Reimplemented in colvarbias_ti.

Definition at line 43 of file colvarbias.C.

References add_colvar, b_output_energy, colvarmodule::bias_by_name, bias_type, biasing_force_scaling_factors, biasing_force_scaling_factors_bin, colvar_forces, colvar_values, colvars, COLVARS_INPUT_ERROR, conf, colvarmodule::debug, colvardeps::description, colvardeps::enable, colvarmodule::error, colvardeps::f_cvb_active, colvardeps::f_cvb_bypass_ext_lagrangian, colvardeps::f_cvb_scale_biasing_force, colvardeps::f_cvb_step_zero_data, colvarparse::get_keyval, colvardeps::get_keyval_feature, colvardeps::is_enabled, colvarmodule::log, name, NULL, num_variables, output_freq, colvarmodule::output_prefix, output_prefix, colvarparse::parse_echo, previous_colvar_forces, colvardeps::print_state, rank, colvar_grid_scalar::read_multicol, colvarparse::set_string, colvardeps::time_step_factor, and colvarmodule::to_str.

Referenced by colvarbias_restraint_histogram::init, colvarbias_restraint::init, colvarbias_meta::init, colvarbias_histogram::init, colvarbias_alb::init, and colvarbias_abf::init.

int colvarbias::init_dependencies ( ) [virtual]

\brief Initialize dependency tree.

Implements colvardeps.

Definition at line 143 of file colvarbias.C.

Referenced by colvarbias.

virtual std::vector<feature *>& colvarbias::modify_features ( ) [inline, virtual]

Implements colvardeps.

Definition at line 217 of file colvarbias.h.

References cvb_features.

Referenced by init_dependencies.

size_t colvarbias::num_variables ( ) const [inline]

How many variables are defined for this bias.

Definition at line 40 of file colvarbias.h.

References colvars.

std::istream & colvarbias::read_state ( std::istream & is )

Read the bias configuration from a restart file or other stream.

Definition at line 516 of file colvarbias.C.

References bias_type, COLVARS_INPUT_ERROR, conf, colvarmodule::error, colvarmodule::log, matching_state, name, read_state_data, set_state_params, state_file_step, and state_keyword.

Referenced by read_state_prefix, and read_state_string.

virtual std::istream& colvarbias::read_state_data ( std::istream & is ) [inline, virtual]

Read all mutable data not already set by set_state_params().

Reimplemented in colvarbias_ti.

Definition at line 146 of file colvarbias.h.

Referenced by read_state.

std::istream & colvarbias::read_state_data_key ( std::istream & is,

char const * key

)

Read a keyword from the state data (typically a header)

Parameters:: Input stream

Keyword labeling the header block.

Definition at line 638 of file colvarbias.C.

References bias_type, COLVARS_INPUT_ERROR, colvarmodule::error, and colvarparse::to_lower_cppstr.

Referenced by colvarbias_reweightaMD::read_state_data, colvarbias_histogram::read_state_data, and colvarbias_ti::read_state_data.

int colvarbias::read_state_prefix ( std::string const & prefix )

Read the bias state from a file with this name or prefix.

Definition at line 597 of file colvarbias.C.

References colvarproxy_io::close_input_stream, COLVARS_FILE_ERROR, colvarproxy_io::input_stream, colvarmodule::main, colvarmodule::proxy, and read_state.

int colvarbias::read_state_string ( char const * buffer )

Read the bias state from this string buffer.

Definition at line 615 of file colvarbias.C.

References COLVARS_BUG_ERROR, COLVARS_FILE_ERROR, colvarmodule::debug, colvarmodule::error, colvarmodule::log, name, NULL, and read_state.

int colvarbias::replica_share ( ) [virtual]

Definition at line 449 of file colvarbias.C.

References COLVARS_NOT_IMPLEMENTED, and colvarmodule::error.

Referenced by colvarbias_abf::update.

int colvarbias::reset ( ) [virtual]

\brief Set to zero all mutable data.

Definition at line 224 of file colvarbias.C.

References bias_energy, colvar_forces, and num_variables.

Referenced by colvarbias.

int colvarbias::set_state_params ( std::string const & state_conf ) [virtual]

Read the values of specific mutable properties from a string.

Reimplemented in colvarbias_ti.

Definition at line 465 of file colvarbias.C.

References bias_type, COLVARS_INPUT_ERROR, conf, colvarmodule::debug, colvarmodule::error, colvarparse::get_keyval, colvarmodule::log, matching_state, name, colvarparse::parse_silent, and state_file_step.

Referenced by read_state, colvarbias_restraint::set_state_params, colvarbias_meta::set_state_params, and colvarbias_alb::set_state_params.

virtual int colvarbias::setup_output ( ) [inline, virtual]

(Re)initialize the output files (does not write them yet).

Reimplemented in colvarbias_meta.

Definition at line 181 of file colvarbias.h.

int colvarbias::update ( ) [virtual]

Retrieve colvar values and calculate their biasing forces Some implementations may use calc_energy() and calc_forces().

Reimplemented in colvarbias_ti.

Definition at line 325 of file colvarbias.C.

References bias_type, calc_energy, calc_forces, colvar_values, colvars, colvarmodule::debug, has_data, colvarmodule::log, NULL, and num_variables.

Referenced by colvarproxy_smp::smp_biases_loop, colvarproxy_smp::smp_biases_script_loop, colvarbias_restraint::update, colvarbias_meta::update, colvarbias_reweightaMD::update, and colvarbias_histogram::update.

colvar* colvarbias::variables ( int i ) const [inline]

Access the i-th variable.

Definition at line 52 of file colvarbias.h.

References colvars.

std::vector<colvar *>* colvarbias::variables ( ) [inline]

Access the variables vector.

Definition at line 46 of file colvarbias.h.

References colvars.

virtual int colvarbias::write_output_files ( ) [inline, virtual]

Write any output files that this bias may have (e.g. PMF files).

Reimplemented in colvarbias_ti.

Definition at line 190 of file colvarbias.h.

std::ostream & colvarbias::write_state ( std::ostream & os )

Write the bias configuration to a state file or other stream.

Definition at line 495 of file colvarbias.C.

References colvarmodule::debug, get_state_params, colvarmodule::log, name, state_keyword, and write_state_data.

Referenced by colvarbias_meta::write_replica_state_file, write_state_prefix, and write_state_string.

virtual std::ostream& colvarbias::write_state_data ( std::ostream & os ) [inline, virtual]

Write all mutable data not already written by get_state_params().

Reimplemented in colvarbias_ti.

Definition at line 140 of file colvarbias.h.

Referenced by write_state.

int colvarbias::write_state_prefix ( std::string const & prefix )

Write the bias state to a file with the given prefix.

Definition at line 568 of file colvarbias.C.

References COLVARS_FILE_ERROR, colvarmodule::state_file_prefix, and write_state.

int colvarbias::write_state_string ( std::string & output )

Write the bias state to a string.

Definition at line 585 of file colvarbias.C.

References COLVARS_FILE_ERROR, colvarmodule::error, name, and write_state.

virtual int colvarbias::write_state_to_replicas ( ) [inline, virtual]

If this bias is communicating with other replicas through files, send it to them.

Reimplemented in colvarbias_meta.

Definition at line 199 of file colvarbias.h.

std::ostream & colvarbias::write_traj ( std::ostream & os ) [virtual]

Output quantities such as the bias energy to the trajectory file.

Reimplemented in colvarbias_alb.

Definition at line 668 of file colvarbias.C.

References bias_energy.

Referenced by colvarbias_restraint::write_traj.

std::ostream & colvarbias::write_traj_label ( std::ostream & os ) [virtual]

Write a label to the trajectory file (comment line).

Reimplemented in colvarbias_alb.

Definition at line 658 of file colvarbias.C.

References colvarmodule::wrap_string.

Referenced by colvarbias_restraint::write_traj_label.

bool colvarbias::b_output_energy [protected]

Whether to write the current bias energy from this bias to the trajectory file.

Definition at line 248 of file colvarbias.h.

Referenced by colvarbias, and init.

cvm::real colvarbias::bias_energy [protected]

\brief Current energy of this bias (colvar_forces should be obtained by deriving this).

Definition at line 245 of file colvarbias.h.

Referenced by colvarbias_meta::calc_energy, calc_energy, colvarbias_restraint_linear::energy_difference, colvarbias_restraint_harmonic::energy_difference, get_energy, reset, colvarbias_restraint_histogram::update, colvarbias_restraint::update, colvarbias_alb::update, colvarbias_restraint_histogram::write_traj, colvarbias_alb::write_traj, and write_traj.

std::string colvarbias::bias_type

Keyword indicating the type of this bias.

Definition at line 28 of file colvarbias.h.

Referenced by colvarbias, init, read_state, read_state_data_key, set_state_params, and update.

colvar_grid_scalar* colvarbias::biasing_force_scaling_factors [protected]

\brief The biasing forces will be scaled by the factor in this grid if b_bias_force_scaled is true.

Definition at line 262 of file colvarbias.h.

Referenced by clear, colvarbias, communicate_forces, and init.

std::vector<int> colvarbias::biasing_force_scaling_factors_bin [protected]

Definition at line 263 of file colvarbias.h.

Referenced by clear, communicate_forces, and init.

std::vector<colvarvalue> colvarbias::colvar_forces [protected]

\brief Current forces from this bias to the variables.

Definition at line 239 of file colvarbias.h.

Referenced by add_colvar, colvarbias_meta::calc_forces, calc_forces, communicate_forces, init, reset, colvarbias_restraint_histogram::update, colvarbias_restraint::update, colvarbias_alb::update, colvarbias_abf::update, colvarbias_restraint_centers_moving::update_acc_work, and colvarbias_meta::update_replicas_registry.

std::vector<colvarvalue> colvarbias::colvar_values [protected]

\brief Up to date value of each colvar.

Definition at line 236 of file colvarbias.h.

Referenced by colvarbias_meta::calc_hills, colvarbias_meta::calc_hills_force, init, update, and colvarbias_meta::update_bias.

std::vector<colvar *> colvarbias::colvars [protected]

\brief Pointers to collective variables to which the bias is applied; current values and metric functions will be obtained through each colvar object.

Definition at line 233 of file colvarbias.h.

Referenced by add_colvar, clear, colvarbias_meta::init, colvarbias_reweightaMD::init, colvarbias_histogram::init, colvarbias_alb::init, colvarbias_abf::init, init, colvarbias_meta::init_ebmeta_params, colvarbias_ti::init_grids, num_variables, colvarbias_meta::read_state_data, colvarbias_alb::update, colvarbias_abf::update, update, colvarbias_meta::update_replicas_registry, variables, and colvarbias_alb::write_traj_label.