Metadynamics bias (implementation of colvarbias) More...

#include <colvarbias_meta.h>

Inheritance diagram for colvarbias_meta:

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Collaboration diagram for colvarbias_meta:

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Classes
class	hill
	A hill for the metadynamics bias. More...

Public Types
enum	Communication { single_replica , multiple_replicas }
	Communication between different replicas. More...

typedef std::list< hill >::iterator	hill_iter

Public Types inherited from colvarparse
enum	Parse_Mode { parse_null = 0 , parse_echo = (1<<1) , parse_echo_default = (1<<2) , parse_deprecation_warning = (1<<3) , parse_silent = 0 , parse_required = (1<<16) , parse_override = (1<<17) , parse_restart = (1<<18) , parse_normal = (1<<1) \| (1<<2) \| (1<<17) , parse_deprecated = (1<<1) \| (1<<3) \| (1<<17) }
	How a keyword is parsed in a string. More...

Public Types inherited from colvardeps
enum	features_biases { f_cvb_active , f_cvb_awake , f_cvb_step_zero_data , f_cvb_apply_force , f_cvb_bypass_ext_lagrangian , f_cvb_get_total_force , f_cvb_output_acc_work , f_cvb_history_dependent , f_cvb_time_dependent , f_cvb_scalar_variables , f_cvb_calc_pmf , f_cvb_calc_ti_samples , f_cvb_write_ti_samples , f_cvb_write_ti_pmf , f_cvb_scale_biasing_force , f_cvb_extended , f_cvb_ntot }

enum	features_colvar { f_cv_active , f_cv_awake , f_cv_gradient , f_cv_collect_gradient , f_cv_collect_atom_ids , f_cv_fdiff_velocity , f_cv_total_force , f_cv_total_force_calc , f_cv_subtract_applied_force , f_cv_Jacobian , f_cv_hide_Jacobian , f_cv_extended_Lagrangian , f_cv_external , f_cv_Langevin , f_cv_output_energy , f_cv_output_value , f_cv_output_velocity , f_cv_output_applied_force , f_cv_output_total_force , f_cv_lower_boundary , f_cv_upper_boundary , f_cv_hard_lower_boundary , f_cv_hard_upper_boundary , f_cv_reflecting_lower_boundary , f_cv_reflecting_upper_boundary , f_cv_grid , f_cv_runave , f_cv_corrfunc , f_cv_scripted , f_cv_custom_function , f_cv_periodic , f_cv_single_cvc , f_cv_scalar , f_cv_linear , f_cv_homogeneous , f_cv_multiple_ts , f_cv_ntot }

enum	features_cvc { f_cvc_active , f_cvc_scalar , f_cvc_periodic , f_cvc_width , f_cvc_lower_boundary , f_cvc_upper_boundary , f_cvc_explicit_atom_groups , f_cvc_gradient , f_cvc_explicit_gradient , f_cvc_inv_gradient , f_cvc_Jacobian , f_cvc_one_site_total_force , f_cvc_debug_gradient , f_cvc_pbc_minimum_image , f_cvc_com_based , f_cvc_scalable , f_cvc_scalable_com , f_cvc_collect_atom_ids , f_cvc_ntot }

enum	features_atomgroup { f_ag_active , f_ag_center , f_ag_center_origin , f_ag_rotate , f_ag_fitting_group , f_ag_explicit_gradient , f_ag_fit_gradients , f_ag_atom_forces , f_ag_scalable , f_ag_scalable_com , f_ag_collect_atom_ids , f_ag_ntot }

Public Member Functions
	colvarbias_meta (char const *key)

virtual int	init (std::string const &conf)
	Parse config string and (re)initialize. More...

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

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

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

virtual int	clear_state_data ()
	Delete only the allocatable data (save memory) More...

virtual int	update ()

virtual int	update_grid_params ()

virtual int	update_bias ()

virtual int	update_grid_data ()

virtual int	replica_share ()

virtual size_t	replica_share_freq () const
	Report the frequency at which this bias needs to communicate with replicas. More...

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

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

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() to a formatted stream. More...

virtual cvm::memory_stream &	write_state_data (cvm::memory_stream &os)
	Write all mutable data not already written by get_state_params() to an unformatted stream. More...

virtual std::istream &	read_state_data (std::istream &is)
	Read all mutable data not already set by set_state_params() from a formatted stream. More...

virtual cvm::memory_stream &	read_state_data (cvm::memory_stream &is)
	Read all mutable data not already set by set_state_params() from an unformatted stream. More...

void	rebin_grids_after_restart ()
	Function called by read_state_data() to execute rebinning (if requested)

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 void	write_pmf ()

virtual int	write_state_to_replicas ()
	If this bias is communicating with other replicas through files, send it to them. More...

Public Member Functions inherited from colvarbias
int	add_colvar (std::string const &cv_name)
	Add a new collective variable to this bias.

size_t	num_variables () const
	How many variables are defined for this bias.

std::vector< colvar * > *	variables ()
	Access the variables vector.

colvar *	variables (int i) const
	Access the i-th variable.

virtual int	update ()

virtual bool	can_accumulate_data ()

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

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

int	communicate_forces ()
	Send forces to the collective variables.

virtual int	end_of_step ()
	Carry out operations needed before next step is run.

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	local_sample_count (int radius)
	Return the average number of samples in a given "radius" around current bin. More...

virtual int	replica_share ()

virtual size_t	replica_share_freq () const
	Report the frequency at which this bias needs to communicate with replicas. More...

virtual void	analyze ()
	Perform analysis tasks.

	colvarbias (char const *key)
	Constructor.

virtual int	init (std::string const &conf)
	Parse config string and (re)initialize. More...

virtual int	init_dependencies ()
	Initialize dependency tree. More...

virtual int	reset ()
	Set to zero all mutable data.

virtual int	clear ()
	Delete everything.

virtual int	clear_state_data ()
	Delete only the allocatable data (save memory) More...

virtual	~colvarbias ()
	Destructor.

virtual std::string const	get_state_params () const
	Write the values of specific mutable properties to a string. More...

int	check_matching_state (std::string const &conf)
	Check the name of the bias vs. the given string, set the matching_state flag accordingly.

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() to a formatted stream. More...

virtual cvm::memory_stream &	write_state_data (cvm::memory_stream &os)
	Write all mutable data not already written by get_state_params() to an unformatted stream. More...

virtual std::istream &	read_state_data (std::istream &is)
	Read all mutable data not already set by set_state_params() from a formatted stream. More...

virtual cvm::memory_stream &	read_state_data (cvm::memory_stream &is)
	Read all mutable data not already set by set_state_params() from an unformatted stream. More...

std::ostream &	write_state_data_key (std::ostream &os, std::string const &key, bool header=true)

cvm::memory_stream &	write_state_data_key (cvm::memory_stream &os, std::string const &key, bool header=true)

std::istream &	read_state_data_key (std::istream &is, std::string const &key)

cvm::memory_stream &	read_state_data_key (cvm::memory_stream &is, std::string const &key)

std::ostream &	write_state (std::ostream &os)
	Write the bias configuration to a formatted stream.

cvm::memory_stream &	write_state (cvm::memory_stream &os)
	Write the bias configuration to an unformatted stream.

std::istream &	read_state (std::istream &is)
	Read the bias configuration from a formatted stream.

cvm::memory_stream &	read_state (cvm::memory_stream &is)
	Read the bias configuration from an unformatted stream.

int	write_state_prefix (std::string const &prefix)
	Write the bias state to a file with the given prefix.

int	write_state_string (std::string &output)
	Write the bias state to a string.

int	read_state_prefix (std::string const &prefix)
	Read the bias state from a file with this name or prefix.

int	read_state_string (char const *buffer)
	Read the bias state from this string buffer.

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

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

Public Member Functions inherited from colvarparse
	colvarparse ()
	Default constructor.

	colvarparse (const std::string &conf)
	Constructor that stores the object's config string.

void	clear ()
	Set the object ready to parse a new configuration string.

void	set_string (std::string const &conf)
	Set a new config string for this object.

	~colvarparse () override
	Default destructor.

std::string const &	get_config () const
	Get the configuration string (includes comments)

int	check_keywords (std::string &conf, char const *key)
	Check that all the keywords within "conf" are in the list of allowed keywords; this will invoke strip_values() first and then loop over all words.

void	clear_keyword_registry ()
	Use this after parsing a config string (note that check_keywords() calls it already)

bool	get_keyval (std::string const &conf, char const *key, int &value, int const &def_value=0, Parse_Mode const parse_mode=parse_normal)

bool	get_keyval (std::string const &conf, char const *key, size_t &value, size_t const &def_value=0, Parse_Mode const parse_mode=parse_normal)

bool	get_keyval (std::string const &conf, char const *key, long &value, long const &def_value=0, Parse_Mode const parse_mode=parse_normal)

bool	get_keyval (std::string const &conf, char const *key, cvm::step_number &value, cvm::step_number const &def_value=0, Parse_Mode const parse_mode=parse_normal)

bool	get_keyval (std::string const &conf, char const *key, std::string &value, std::string const &def_value=std::string(""), Parse_Mode const parse_mode=parse_normal)

bool	get_keyval (std::string const &conf, char const *key, cvm::real &value, cvm::real const &def_value=0.0, Parse_Mode const parse_mode=parse_normal)

bool	get_keyval (std::string const &conf, char const *key, cvm::rvector &value, cvm::rvector const &def_value=cvm::rvector(), Parse_Mode const parse_mode=parse_normal)

bool	get_keyval (std::string const &conf, char const *key, cvm::quaternion &value, cvm::quaternion const &def_value=cvm::quaternion(), Parse_Mode const parse_mode=parse_normal)

bool	get_keyval (std::string const &conf, char const *key, colvarvalue &value, colvarvalue const &def_value=colvarvalue(colvarvalue::type_notset), Parse_Mode const parse_mode=parse_normal)

bool	get_keyval (std::string const &conf, char const *key, bool &value, bool const &def_value=false, Parse_Mode const parse_mode=parse_normal)

bool	get_keyval (std::string const &conf, char const *key, std::vector< int > &values, std::vector< int > const &def_values=std::vector< int >(0, 0), Parse_Mode const parse_mode=parse_normal)

bool	get_keyval (std::string const &conf, char const *key, std::vector< size_t > &values, std::vector< size_t > const &def_values=std::vector< size_t >(0, 0), Parse_Mode const parse_mode=parse_normal)

bool	get_keyval (std::string const &conf, char const *key, std::vector< long > &values, std::vector< long > const &def_values=std::vector< long >(0, 0), Parse_Mode const parse_mode=parse_normal)

bool	get_keyval (std::string const &conf, char const *key, std::vector< std::string > &values, std::vector< std::string > const &def_values=std::vector< std::string >(0, std::string("")), Parse_Mode const parse_mode=parse_normal)

bool	get_keyval (std::string const &conf, char const *key, std::vector< cvm::real > &values, std::vector< cvm::real > const &def_values=std::vector< cvm::real >(0, 0.0), Parse_Mode const parse_mode=parse_normal)

bool	get_keyval (std::string const &conf, char const *key, std::vector< cvm::rvector > &values, std::vector< cvm::rvector > const &def_values=std::vector< cvm::rvector >(0, cvm::rvector()), Parse_Mode const parse_mode=parse_normal)

bool	get_keyval (std::string const &conf, char const *key, std::vector< cvm::quaternion > &values, std::vector< cvm::quaternion > const &def_values=std::vector< cvm::quaternion >(0, cvm::quaternion()), Parse_Mode const parse_mode=parse_normal)

bool	get_keyval (std::string const &conf, char const *key, std::vector< colvarvalue > &values, std::vector< colvarvalue > const &def_values=std::vector< colvarvalue >(0, colvarvalue(colvarvalue::type_notset)), Parse_Mode const parse_mode=parse_normal)

bool	key_lookup (std::string const &conf, char const key, std::string data=nullptr, size_t *save_pos=nullptr)
	Low-level function for parsing configuration strings; automatically adds the requested keyword to the list of valid ones. More...

std::istream &	read_config_line (std::istream &is, std::string &line)
	Reads a configuration line, adds it to config_string, and returns the stream. More...

template<>
int	_get_keyval_scalar_value_ (std::string const &key_str, std::string const &data, bool &value, bool const &)

template<>
int	_get_keyval_scalar_novalue_ (std::string const &key_str, bool &value, Parse_Mode const &parse_mode)

Public Member Functions inherited from colvarparams
int	param_exists (std::string const &param_name)
	Whether the parameter param_name exists.

virtual std::vector< std::string >	get_param_names ()
	Get a copy of the names of registered parameters.

virtual std::vector< std::string >	get_param_grad_names ()
	Get a copy of the names of registered parameter gradients.

virtual void const *	get_param_ptr (std::string const &param_name)
	Pointer to the parameter param_name.

virtual void const *	get_param_grad_ptr (std::string const &param_name)
	Pointer to the gradient of parameter param_name.

virtual cvm::real	get_param (std::string const &param_name)
	Value of the parameter param_name (must be a scalar)

virtual int	set_param (std::string const &param_name, void const *new_value)
	Set the named parameter to the given value. More...

Public Member Functions inherited from colvardeps
int	get_time_step_factor () const
	returns time_step_factor

void	init_feature (int feature_id, const char *description, feature_type type)
	Pair a numerical feature ID with a description and type.

bool	is_not_set (int id)

bool	is_dynamic (int id)

bool	is_static (int id)

bool	is_user (int id)

virtual const std::vector< feature * > &	features () const =0

virtual std::vector< feature * > &	modify_features ()=0

void	add_child (colvardeps *child)

void	remove_child (colvardeps *child)

void	remove_all_children ()

bool	is_enabled (int f=f_cv_active) const

bool	is_available (int f=f_cv_active) const

void	provide (int feature_id, bool truefalse=true)

void	set_enabled (int feature_id, bool truefalse=true)
	Enable or disable, depending on flag value.

int	enable (int f, bool dry_run=false, bool toplevel=true)

int	disable (int f)

void	free_children_deps ()

void	restore_children_deps ()
	re-enable children features (to be used when object becomes active)

int	decr_ref_count (int f)

virtual void	do_feature_side_effects (int)

virtual int	init_dependencies ()=0
	Initialize dependency tree for object of a derived class. More...

void	require_feature_self (int f, int g)
	Make feature f require feature g within the same object.

void	exclude_feature_self (int f, int g)
	Make features f and g mutually exclusive within the same object.

void	require_feature_children (int f, int g)
	Make feature f require feature g within children.

void	require_feature_alt (int f, int g, int h)
	Make feature f require either g or h within the same object.

void	require_feature_alt (int f, int g, int h, int i)
	Make feature f require any of g, h, or i within the same object.

void	require_feature_alt (int f, int g, int h, int i, int j)
	Make feature f require any of g, h, i, or j within the same object.

void	print_state ()
	print all enabled features and those of children, for debugging

void	check_enabled (int f, std::string const &reason) const
	Check that a feature is enabled, raising COLVARS_BUG_ERROR if not.

Public Member Functions inherited from colvarbias_ti
	colvarbias_ti (char const *key)

virtual int	init (std::string const &conf)
	Parse config string and (re)initialize. More...

virtual int	init_grids ()

virtual int	update ()

virtual int	update_system_forces (std::vector< colvarvalue > const *subtract_forces)

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() to a formatted stream. More...

virtual cvm::memory_stream &	write_state_data (cvm::memory_stream &os)
	Write all mutable data not already written by get_state_params() to an unformatted stream. More...

virtual std::istream &	read_state_data (std::istream &is)
	Read all mutable data not already set by set_state_params() from a formatted stream. More...

virtual cvm::memory_stream &	read_state_data (cvm::memory_stream &is)
	Read all mutable data not already set by set_state_params() from an unformatted stream. More...

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

Public Attributes
Communication	comm
	Communication between different replicas.

Public Attributes inherited from colvarbias
std::string	name
	Name of this bias.

std::string	bias_type
	Keyword indicating the type of this bias.

std::string	state_keyword
	Keyword used in state files (== bias_type most of the time)

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

size_t	output_freq
	Frequency for writing output files.

std::string	output_prefix
	Use this prefix for all output files.

Public Attributes inherited from colvardeps
std::string	description

Protected Member Functions
std::string const	hills_traj_file_name () const
	Name of the hill logfile.

void	recount_hills_off_grid (hill_iter h_first, hill_iter h_last, colvar_grid_scalar *ge)
	Regenerate the hills_off_grid list.

template<typename OST >
OST &	write_hill_template_ (OST &os, colvarbias_meta::hill const &h)

std::ostream &	write_hill (std::ostream &os, hill const &h)
	Write a hill to a formatted stream.

cvm::memory_stream &	write_hill (cvm::memory_stream &os, hill const &h)
	Write a hill to an unformatted stream.

template<typename IST >
IST &	read_hill_template_ (IST &is)

std::istream &	read_hill (std::istream &is)
	Read a new hill from a formatted stream.

cvm::memory_stream &	read_hill (cvm::memory_stream &is)
	Read a new hill from an unformatted stream.

std::list< hill >::const_iterator	add_hill (hill const &h)
	Add a new hill; if a .hills trajectory is written, write it there; if there is more than one replica, communicate it to the others.

std::list< hill >::const_iterator	delete_hill (hill_iter &h)
	Remove a previously saved hill (returns an iterator for the next hill in the list)

virtual void	calc_hills (hill_iter h_first, hill_iter h_last, cvm::real &energy, std::vector< colvarvalue > const *values)
	Calculate the values of the hills, incrementing bias_energy.

virtual void	calc_hills_force (size_t const &i, hill_iter h_first, hill_iter h_last, std::vector< colvarvalue > &forces, std::vector< colvarvalue > const *values)
	Calculate the forces acting on the i-th colvar, incrementing colvar_forces[i]; must be called after calc_hills each time the values of the colvars are changed.

void	project_hills (hill_iter h_first, hill_iter h_last, colvar_grid_scalar ge, colvar_grid_gradient gf, bool print_progress=false)
	Project the selected hills onto grids.

virtual int	update_replicas_registry ()
	Read the existing replicas on registry.

virtual int	read_replica_files ()
	Read new data from replicas' files.

virtual int	write_replica_state_file ()
	Write full state information to be read by other replicas.

virtual int	reopen_replica_buffer_file ()
	Call this after write_replica_state_file()

Protected Member Functions inherited from colvarparse
bool	get_key_string_value (std::string const &conf, char const *key, std::string &data)
	Get the string value of a keyword, and save it for later parsing.

bool	get_key_string_multi_value (std::string const &conf, char const *key, std::vector< std::string > &data)
	Get multiple strings from repeated instances of a same keyword.

template<typename TYPE >
bool	_get_keyval_scalar_ (std::string const &conf, char const *key, TYPE &value, TYPE const &def_value, Parse_Mode const &parse_mode)
	Template for single-value keyword parsers.

template<typename TYPE >
bool	_get_keyval_vector_ (std::string const &conf, char const *key, std::vector< TYPE > &values, std::vector< TYPE > const &def_values, Parse_Mode const &parse_mode)
	Template for multiple-value keyword parsers.

template<typename TYPE >
int	_get_keyval_scalar_value_ (std::string const &key_str, std::string const &data, TYPE &value, TYPE const &def_value)
	Extract the value of a variable from a string.

template<typename TYPE >
int	_get_keyval_scalar_novalue_ (std::string const &key_str, TYPE &value, Parse_Mode const &parse_mode)
	Handle the case where the user provides a keyword without value.

template<typename TYPE >
void	mark_key_set_user (std::string const &key_str, TYPE const &value, Parse_Mode const &parse_mode)
	Record that the keyword has just been user-defined.

template<typename TYPE >
void	mark_key_set_default (std::string const &key_str, TYPE const &def_value, Parse_Mode const &parse_mode)
	Record that the keyword has just been set to its default value.

void	error_key_required (std::string const &key_str, Parse_Mode const &parse_mode)
	Raise error condition due to the keyword being required!

bool	key_already_set (std::string const &key_str)
	True if the keyword has been set already.

void	add_keyword (char const *key)
	Add a new valid keyword to the list.

void	strip_values (std::string &conf)
	Remove all the values from the config string.

Protected Member Functions inherited from colvarparams
	colvarparams ()
	Default constructor.

virtual	~colvarparams ()
	Default destructor.

void	register_param (std::string const &param_name, void *param_ptr)
	Register the given parameter.

void	register_param_grad (std::string const &param_name, colvarvalue *param_grad_ptr)
	Register the gradient of the given parameter.

Protected Member Functions inherited from colvardeps
bool	get_keyval_feature (colvarparse cvp, std::string const &conf, char const key, int feature_id, bool const &def_value, colvarparse::Parse_Mode const parse_mode=colvarparse::parse_normal)
	Parse a keyword and enable a feature accordingly.

Protected Attributes
cvm::real	hill_width

std::vector< cvm::real >	colvar_sigmas
	The sigma parameters of the Gaussian hills.

size_t	new_hill_freq
	Number of simulation steps between two hills.

bool	b_hills_traj
	Write the hill logfile.

std::list< hill >	hills
	List of hills used on this bias (total); if a grid is employed, these don't need to be updated at every time step.

hill_iter	new_hills_begin
	Iterator to the first of the "newest" hills (when using grids, those who haven't been mapped yet)

std::list< hill >	hills_off_grid
	List of hills used on this bias that are on the boundary edges; these are updated regardless of whether hills are used.

hill_iter	new_hills_off_grid_begin
	Same as new_hills_begin, but for the off-grid ones.

cvm::real	hill_weight
	Height of new hills.

bool	use_grids
	Bin the hills on grids of energy and forces, and use them to force the colvars (as opposed to deriving the hills analytically)

bool	rebin_grids
	Rebin the hills upon restarting.

bool	expand_grids
	Should the grids be expanded if necessary?

size_t	grids_freq
	How often the hills should be projected onto the grids.

bool	keep_hills
	Keep hills in the restart file (e.g. to accurately rebin later)

bool	restart_keep_hills
	value of keepHills saved in the most recent restart file

bool	dump_fes
	Dump the free energy surface (.pmf file) every restartFrequency.

bool	dump_replica_fes
	Dump the free energy surface (.pmf file) every restartFrequency using only the hills from this replica (only applicable to more than one replica)

bool	dump_fes_save
	Dump the free energy surface files at different time steps, appending the step number to each file.

bool	well_tempered
	Whether to use well-tempered metadynamics.

cvm::real	bias_temperature
	Biasing temperature in well-tempered metadynamics.

bool	ebmeta
	Ensemble-biased metadynamics (EBmeta) flag.

colvar_grid_scalar *	target_dist
	Target distribution for EBmeta.

cvm::step_number	ebmeta_equil_steps
	Number of equilibration steps for EBmeta.

bool	safely_read_restart
	Try to read the restart information by allocating new grids before replacing the current ones (used e.g. in multiple_replicas)

colvar_grid_scalar *	hills_energy
	Hill energy, cached on a grid.

colvar_grid_gradient *	hills_energy_gradients
	Hill forces, cached on a grid.

std::string	replica_id
	Identifier for this replica.

std::string	replica_file_name
	File containing the paths to the output files from this replica.

std::vector< colvarbias_meta * >	replicas
	Additional, "mirror" metadynamics biases, to collect info from the other replicas. More...

size_t	replica_update_freq = 0
	Frequency at which data the "mirror" biases are updated.

std::string	replicas_registry_file

std::string	replicas_registry
	List of replicas (and their output list files)

std::string	replica_list_file
	List of files written by this replica.

std::string	replica_state_file

bool	replica_state_file_in_sync
	Whether a mirror bias has read the latest version of its state file.

size_t	update_status

std::string	replica_hills_file

std::streampos	replica_hills_file_pos
	Position within replica_hills_file (when reading it)

std::ostringstream	hills_traj_os_buf
	Cache of the hills trajectory.

Protected Attributes inherited from colvarbias
std::vector< colvar * >	colvars
	Pointers to collective variables to which the bias is applied; current values and metric functions will be obtained through each colvar object.

std::vector< colvarvalue >	colvar_values
	Up to date value of each colvar.

std::vector< colvarvalue >	colvar_forces
	Current forces from this bias to the variables.

std::vector< colvarvalue >	previous_colvar_forces
	Forces last applied by this bias to the variables.

cvm::real	bias_energy
	Current energy of this bias (colvar_forces should be obtained by deriving this)

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

bool	has_data
	Whether this bias has already accumulated information (for history-dependent biases)

cvm::step_number	state_file_step
	Step number read from the last state file.

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

colvar_grid_scalar *	biasing_force_scaling_factors
	The biasing forces will be scaled by the factor in this grid if b_bias_force_scaled is true.

std::vector< int >	biasing_force_scaling_factors_bin

Protected Attributes inherited from colvarparse
std::string const	keyword_delimiters_left
	Characters allowed immediately to the left of a kewyord.

std::string const	keyword_delimiters_right
	Characters allowed immediately to the right of a kewyord.

std::list< std::string >	allowed_keywords
	List of legal keywords for this object: this is updated by each call to colvarparse::get_keyval() or colvarparse::key_lookup()

std::map< std::string, key_set_mode >	key_set_modes
	Track which keywords have been already set, and how.

std::list< size_t >	data_begin_pos
	List of delimiters for the values of each keyword in the configuration string; all keywords will be stripped of their values before the keyword check is performed.

std::list< size_t >	data_end_pos
	List of delimiters for the values of each keyword in the configuration string; all keywords will be stripped of their values before the keyword check is performed.

std::string	config_string
	Configuration string of the object (includes comments)

Protected Attributes inherited from colvarparams
std::map< std::string, void const * >	param_map
	Pointers to relevant parameters that may be accessed by other objects.

std::map< std::string, colvarvalue const * >	param_grad_map
	Derivatives of the object with respect to internal parameters.

Protected Attributes inherited from colvardeps
int	time_step_factor

std::vector< feature_state >	feature_states
	List of the states of all features.

Protected Attributes inherited from colvarbias_ti
std::vector< colvarvalue >	ti_system_forces
	Forces exerted from the system to the associated variables.

std::shared_ptr< colvar_grid_gradient >	ti_avg_forces
	Averaged system forces.

std::shared_ptr< colvar_grid_count >	ti_count
	Histogram of sampled data.

std::vector< int >	ti_bin

Private Member Functions
template<typename IST , typename GT >
IST &	read_grid_data_template_ (IST &is, std::string const &key, GT grid, GT backup_grid)

template<typename IST >
IST &	read_state_data_template_ (IST &is)

template<typename OST >
OST &	write_state_data_template_ (OST &os)

Additional Inherited Members
Static Public Member Functions inherited from colvarbias
static void	delete_features ()

Static Public Member Functions inherited from colvarparse
static std::string	to_lower_cppstr (std::string const &in)
	Return a lowercased copy of the string.

static std::istream &	getline_nocomments (std::istream &is, std::string &s)
	Works as std::getline() but also removes everything between a comment character and the following newline.

static int	check_braces (std::string const &conf, size_t const start_pos)
	Check if the content of a config string has matching braces. More...

static int	check_ascii (std::string const &conf)
	Check that a config string contains non-ASCII characters. More...

static void	split_string (const std::string &data, const std::string &delim, std::vector< std::string > &dest)
	Split a string with a specified delimiter into a vector. More...

Static Public Attributes inherited from colvarbias
static std::vector< feature * >	cvb_features
	Implementation of the feature list for colvarbias.

Static Public Attributes inherited from colvarparse
static const char *const	white_space = " \t"
	Accepted white space delimiters, used in key_lookup()

Protected Types inherited from colvarparse
enum	key_set_mode { key_not_set = 0 , key_set_user = 1 , key_set_default = 2 }
	How a keyword has been set.

Protected Types inherited from colvardeps
enum	feature_type { f_type_not_set , f_type_dynamic , f_type_user , f_type_static }
	Enum of possible feature types.

Detailed Description

Metadynamics bias (implementation of colvarbias)

Member Enumeration Documentation

◆ Communication

enum colvarbias_meta::Communication

Communication between different replicas.

Enumerator
single_replica	One replica (default)
multiple_replicas	Hills added concurrently by several replicas.

Member Function Documentation

◆ calc_energy()

int colvarbias_meta::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

Reimplemented from colvarbias.

◆ calc_forces()

int colvarbias_meta::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 from colvarbias.

◆ clear_state_data()

int colvarbias_meta::clear_state_data ( )

virtual

Delete only the allocatable data (save memory)

Reimplemented from colvarbias.

◆ get_state_params()

std::string const colvarbias_meta::get_state_params ( ) const

virtual

Write the values of specific mutable properties to a string.

Reimplemented from colvarbias.

◆ init()

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

virtual

Parse config string and (re)initialize.

Reimplemented from colvarbias.

◆ read_state_data() [1/2]

cvm::memory_stream & colvarbias_meta::read_state_data ( cvm::memory_stream & is )

virtual

Read all mutable data not already set by set_state_params() from an unformatted stream.

Reimplemented from colvarbias.

◆ read_state_data() [2/2]

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

virtual

Read all mutable data not already set by set_state_params() from a formatted stream.

Reimplemented from colvarbias.

◆ replica_share()

int colvarbias_meta::replica_share ( )

virtual

Reimplemented from colvarbias.

◆ replica_share_freq()

size_t colvarbias_meta::replica_share_freq ( ) const

virtual

Report the frequency at which this bias needs to communicate with replicas.

Reimplemented from colvarbias.

◆ set_state_params()

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

virtual

Read the values of specific mutable properties from a string.

Reimplemented from colvarbias.

◆ setup_output()

int colvarbias_meta::setup_output ( )

virtual

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

Reimplemented from colvarbias.

◆ update()

int colvarbias_meta::update ( )

virtual

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

Reimplemented from colvarbias.

◆ write_output_files()

int colvarbias_meta::write_output_files ( )

virtual

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

Reimplemented from colvarbias.

◆ write_state_data() [1/2]

cvm::memory_stream & colvarbias_meta::write_state_data ( cvm::memory_stream & os )

virtual

Write all mutable data not already written by get_state_params() to an unformatted stream.

Reimplemented from colvarbias.

◆ write_state_data() [2/2]

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

virtual

Write all mutable data not already written by get_state_params() to a formatted stream.

Reimplemented from colvarbias.

◆ write_state_to_replicas()

int colvarbias_meta::write_state_to_replicas ( )

virtual

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

Reimplemented from colvarbias.

Member Data Documentation

◆ hill_width

cvm::real colvarbias_meta::hill_width

protected

Width of a hill in number of grid points

The local width of each collective variable, multiplied by this number, provides the hill width along that direction

◆ replica_hills_file

std::string colvarbias_meta::replica_hills_file

protected

Explicit hills communicated between replicas

This file becomes empty after replica_state_file is rewritten

◆ replica_state_file

std::string colvarbias_meta::replica_state_file

protected

Hills energy and gradients written specifically for other replica (in addition to its own restart file)

◆ replicas

std::vector<colvarbias_meta *> colvarbias_meta::replicas

protected

Additional, "mirror" metadynamics biases, to collect info from the other replicas.

These are supposed to be synchronized by reading data from the other replicas, and not be modified by the "local" replica

◆ replicas_registry_file

std::string colvarbias_meta::replicas_registry_file

protected

List of replicas (and their output list files): contents are copied into replicas_registry for convenience

◆ update_status

size_t colvarbias_meta::update_status

protected

If there was a failure reading one of the files (because they are not complete), this counter is incremented

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

colvarbias_meta.h
colvarbias_meta.cpp

Classes

Public Types

Public Member Functions

Public Attributes

Protected Member Functions

Protected Attributes

Private Member Functions

Additional Inherited Members

Detailed Description

Member Enumeration Documentation

◆ Communication

Member Function Documentation

◆ calc_energy()

◆ calc_forces()

◆ clear_state_data()

◆ get_state_params()

◆ init()

◆ read_state_data() [1/2]

◆ read_state_data() [2/2]

◆ replica_share()

◆ replica_share_freq()

◆ set_state_params()

◆ setup_output()

◆ update()

◆ write_output_files()

◆ write_state_data() [1/2]

◆ write_state_data() [2/2]

◆ write_state_to_replicas()

Member Data Documentation

◆ hill_width

◆ replica_hills_file

◆ replica_state_file

◆ replicas

◆ replicas_registry_file

◆ update_status