Collective Variables Module - Developer Documentation
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Public Member Functions | Protected Member Functions | Protected Attributes | List of all members
colvarbias_restraint_k_moving Class Reference

Options to change the restraint force constant over time. More...

#include <colvarbias_restraint.h>

Inheritance diagram for colvarbias_restraint_k_moving:
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Public Member Functions

 colvarbias_restraint_k_moving (char const *key)
 
virtual int init (std::string const &conf)
 Parse config string and (re)initialize. More...
 
virtual int update ()
 
virtual int change_configuration (std::string const &)
 Load new configuration - force constant and/or centers only. More...
 
virtual std::string const get_state_params () const
 
virtual int set_state_params (std::string const &conf)
 
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...
 
- Public Member Functions inherited from colvarbias_restraint_k
 colvarbias_restraint_k (char const *key)
 
virtual int init (std::string const &conf)
 Parse config string and (re)initialize. More...
 
virtual int change_configuration (std::string const &conf)
 Load new configuration - force constant and/or centers only. More...
 
- Public Member Functions inherited from colvarbias_restraint
virtual int update ()
 Retrieve colvar values and calculate their biasing forces. More...
 
virtual int change_configuration (std::string const &)
 Load new configuration - force constant and/or centers only. More...
 
virtual cvm::real energy_difference (std::string const &)
 Calculate change in energy from using alternate configuration. 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 &conf)
 Read the values of specific mutable properties from a string. 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...
 
 colvarbias_restraint (char const *key)
 Constructor.
 
virtual int init (std::string const &conf)
 Parse config string and (re)initialize. 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.
 
colvarvariables (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_streamwrite_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_streamread_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_streamwrite_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_streamread_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_streamwrite_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_streamread_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_streamwrite_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_streamread_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 Member Functions inherited from colvarbias_restraint_moving
 colvarbias_restraint_moving (char const *key)
 
virtual int init (std::string const &conf)
 
virtual int update ()
 
virtual int change_configuration (std::string const &)
 
virtual std::string const get_state_params () const
 
virtual int set_state_params (std::string const &conf)
 

Protected Member Functions

int update_acc_work ()
 Update the accumulated work.
 
- Protected Member Functions inherited from colvarbias_restraint
virtual cvm::real restraint_potential (size_t i) const =0
 Potential function for the i-th colvar. More...
 
virtual colvarvalue const restraint_force (size_t i) const =0
 Force function for the i-th colvar. More...
 
virtual cvm::real d_restraint_potential_dk (size_t i) const =0
 Derivative of the potential function with respect to the force constant. More...
 
- 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 target_force_k
 Restraint force constant (target value)
 
cvm::real starting_force_k
 Restraint force constant (starting value)
 
cvm::real lambda_exp
 Exponent for varying the force constant.
 
cvm::real restraint_FE
 Intermediate quantity to compute the restraint free energy (in TI, would be the accumulating FE derivative)
 
cvm::real target_equil_steps
 Equilibration steps for restraint FE calculation through TI.
 
cvm::real force_k_incr
 Increment of the force constant at each step.
 
- Protected Attributes inherited from colvarbias_restraint_k
cvm::real force_k
 Restraint force constant.
 
bool check_positive_k
 Whether the force constant should be positive.
 
- 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< colvarvaluecolvar_values
 Up to date value of each colvar.
 
std::vector< colvarvaluecolvar_forces
 Current forces from this bias to the variables.
 
std::vector< colvarvalueprevious_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_scalarbiasing_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_modekey_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_statefeature_states
 List of the states of all features.
 
- Protected Attributes inherited from colvarbias_ti
std::vector< colvarvalueti_system_forces
 Forces exerted from the system to the associated variables.
 
std::shared_ptr< colvar_grid_gradientti_avg_forces
 Averaged system forces.
 
std::shared_ptr< colvar_grid_countti_count
 Histogram of sampled data.
 
std::vector< int > ti_bin
 
- Protected Attributes inherited from colvarbias_restraint_moving
bool b_chg_centers
 Moving target?
 
bool b_chg_force_k
 Changing force constant?
 
bool b_decoupling
 Perform decoupling of the restraint?
 
int target_nstages
 Number of stages over which to perform the change If zero, perform a continuous change.
 
int stage
 Number of current stage of the perturbation.
 
std::vector< cvm::reallambda_schedule
 Lambda-schedule for custom varying force constant.
 
cvm::step_number target_nsteps
 Number of steps required to reach the target force constant or restraint centers.
 
cvm::step_number first_step
 Timestep at which the restraint starts moving.
 
cvm::real acc_work
 Accumulated work (computed when outputAccumulatedWork == true)
 

Additional Inherited Members

- 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
}
 
- 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...
 
- 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
 
- 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

Options to change the restraint force constant over time.

Member Function Documentation

◆ change_configuration()

virtual int colvarbias_restraint_k_moving::change_configuration ( std::string const &  )
inlinevirtual

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

Reimplemented from colvarbias_restraint_k.

Reimplemented in colvarbias_restraint_harmonic, and colvarbias_restraint_linear.

◆ get_state_params()

std::string const colvarbias_restraint_k_moving::get_state_params ( ) const
virtual

Reimplemented from colvarbias_restraint_moving.

◆ init()

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

Parse config string and (re)initialize.

Reimplemented from colvarbias_restraint_k.

Reimplemented in colvarbias_restraint_harmonic, colvarbias_restraint_harmonic_walls, and colvarbias_restraint_linear.

◆ set_state_params()

int colvarbias_restraint_k_moving::set_state_params ( std::string const &  conf)
virtual

Reimplemented from colvarbias_restraint_moving.

◆ update()

int colvarbias_restraint_k_moving::update ( )
virtual

Reimplemented from colvarbias_restraint_moving.

◆ write_traj()

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

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

Reimplemented from colvarbias_restraint.

Reimplemented in colvarbias_restraint_harmonic, colvarbias_restraint_harmonic_walls, and colvarbias_restraint_linear.

◆ write_traj_label()

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

Write a label to the trajectory file (comment line)

Reimplemented from colvarbias_restraint.

Reimplemented in colvarbias_restraint_harmonic, colvarbias_restraint_harmonic_walls, and colvarbias_restraint_linear.


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