|
|
| colvarbias_opes (char const *key) |
| | Constructor.
|
| |
| int | init (std::string const &conf) override |
| | Initializer. More...
|
| |
| int | update () override |
| | Per-timestep update. More...
|
| |
| std::ostream & | write_state_data (std::ostream &os) override |
| | Save the state to a text file for restarting. More...
|
| |
| std::istream & | read_state_data (std::istream &is) override |
| | Read the state from a text file for restarting. More...
|
| |
| cvm::memory_stream & | write_state_data (cvm::memory_stream &os) override |
| | Save the state to a binary file for restarting. More...
|
| |
| cvm::memory_stream & | read_state_data (cvm::memory_stream &is) override |
| | Read the state from a binary file for restarting. More...
|
| |
| int | write_output_files () override |
| | Write to files at restart steps. More...
|
| |
|
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) const |
| |
| cvm::memory_stream & | write_state_data_key (cvm::memory_stream &os, std::string const &key, bool header=true) const |
| |
| 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 () |
| |
|
| 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) |
| |
|
int | param_exists (std::string const ¶m_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 ¶m_name) |
| | Pointer to the parameter param_name.
|
| |
|
virtual void const * | get_param_grad_ptr (std::string const ¶m_name) |
| | Pointer to the gradient of parameter param_name.
|
| |
|
virtual cvm::real | get_param (std::string const ¶m_name) |
| | Value of the parameter param_name (must be a scalar)
|
| |
| virtual int | set_param (std::string const ¶m_name, void const *new_value) |
| | Set the named parameter to the given value. More...
|
| |
|
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.
|
| |
|
|
static void | delete_features () |
| |
|
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...
|
| |
|
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.
|
| |
|
std::string | description |
| |
|
static std::vector< feature * > | cvb_features |
| | Implementation of the feature list for colvarbias.
|
| |
|
static const char *const | white_space = " \t" |
| | Accepted white space delimiters, used in key_lookup()
|
| |
| enum | key_set_mode { key_not_set = 0
, key_set_user = 1
, key_set_default = 2
} |
| | How a keyword has been set.
|
| |
| enum | feature_type { f_type_not_set
, f_type_dynamic
, f_type_user
, f_type_static
} |
| | Enum of possible feature types.
|
| |
|
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.
|
| |
|
| colvarparams () |
| | Default constructor.
|
| |
|
virtual | ~colvarparams () |
| | Default destructor.
|
| |
|
void | register_param (std::string const ¶m_name, void *param_ptr) |
| | Register the given parameter.
|
| |
|
void | register_param_grad (std::string const ¶m_name, colvarvalue *param_grad_ptr) |
| | Register the gradient of the given parameter.
|
| |
|
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.
|
| |
|
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 |
| |
|
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)
|
| |
|
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.
|
| |
| int | time_step_factor |
| |
|
std::vector< feature_state > | feature_states |
| | List of the states of all features.
|
| |
Public Member Functions inherited from colvarbias