Grid of values of a function of several collective variables. More...
#include <colvargrid.h>
Inheritance diagram for colvar_grid< T >:
Collaboration diagram for colvar_grid< T >:
Public Member Functions | |
| size_t | address (std::vector< int > const &ix) const |
| Get the low-level index corresponding to an index. | |
| size_t | num_variables () const |
| Return the number of colvar objects. | |
| std::vector< int > const & | number_of_points_vec () const |
| Return the numbers of points in all dimensions. | |
| size_t | number_of_points (int const icv=-1) const |
| std::vector< int > const & | sizes () const |
| Get the sizes in each direction. | |
| void | set_sizes (std::vector< int > const &new_sizes) |
| Set the sizes in each direction. | |
| size_t | multiplicity () const |
| Return the multiplicity of the type used. | |
| void | request_actual_value (bool b=true) |
| Request grid to use actual values of extended coords. | |
| int | setup (std::vector< int > const &nx_i, T const &t=T(), size_t const &mult_i=1) |
| Allocate data. | |
| int | setup () |
| Allocate data (allow initialization also after construction) | |
| void | reset (T const &t=T()) |
| Reset data (in case the grid is being reused) | |
| colvar_grid () | |
| Default constructor. | |
| virtual | ~colvar_grid () |
| Destructor. | |
| colvar_grid (colvar_grid< T > const &g) | |
| "Almost copy-constructor": only copies configuration parameters from another grid, but doesn't reallocate stuff; setup() must be called after that; | |
| colvar_grid (std::vector< int > const &nx_i, T const &t=T(), size_t mult_i=1) | |
| Constructor from explicit grid sizes. More... | |
| colvar_grid (std::vector< colvar * > const &colvars, T const &t=T(), size_t mult_i=1, bool add_extra_bin=false) | |
| Constructor from a vector of colvars. More... | |
| int | init_from_colvars (std::vector< colvar * > const &colvars, size_t mult_i=1, bool add_extra_bin=false) |
| int | init_from_boundaries () |
| void | wrap (std::vector< int > &ix) const |
| bool | wrap_detect_edge (std::vector< int > &ix) const |
| bool | wrap_to_edge (std::vector< int > &ix, std::vector< int > &edge_bin) const |
| int | current_bin_scalar (int const i) const |
| Report the bin corresponding to the current value of variable i. | |
| int | current_bin_flat_bound () const |
| Report the flattened bin address corresponding to the current value of all variables and assign first or last bin if out of boundaries. | |
| int | current_bin_scalar_bound (int const i) const |
| Report the bin corresponding to the current value of variable i and assign first or last bin if out of boundaries. | |
| int | current_bin_scalar (int const i, int const iv) const |
| Report the bin corresponding to the current value of item iv in variable i. | |
| int | value_to_bin_scalar (colvarvalue const &value, const int i) const |
| Use the lower boundary and the width to report which bin the provided value is in. | |
| cvm::real | current_bin_scalar_fraction (int const i) const |
| Report the fraction of bin beyond current_bin_scalar() | |
| cvm::real | value_to_bin_scalar_fraction (colvarvalue const &value, const int i) const |
| Use the lower boundary and the width to report the fraction of bin beyond value_to_bin_scalar() that the provided value is in. | |
| int | value_to_bin_scalar_bound (colvarvalue const &value, const int i) const |
| Use the lower boundary and the width to report which bin the provided value is in and assign first or last bin if out of boundaries. | |
| int | value_to_bin_scalar (colvarvalue const &value, colvarvalue const &new_offset, cvm::real const &new_width) const |
| Same as the standard version, but uses another grid definition. | |
| colvarvalue | bin_to_value_scalar (int const &i_bin, int const i) const |
| Use the two boundaries and the width to report the central value corresponding to a bin index. | |
| colvarvalue | bin_to_value_scalar (int const &i_bin, colvarvalue const &new_offset, cvm::real const &new_width) const |
| Same as the standard version, but uses different parameters. | |
| void | set_value (std::vector< int > const &ix, T const &t, size_t const &imult=0) |
| Set the value at the point with index ix. | |
| void | set_value (size_t i, T const &t) |
| Set the value at the point with linear address i (for speed) | |
| T | get_value (size_t i) const |
| Get the value at the point with linear address i (for speed) | |
| void | delta_grid (colvar_grid< T > const &other_grid) |
| Get the change from this to other_grid and store the result in this. this_grid := other_grid - this_grid Grids must have the same dimensions. | |
| void | copy_grid (colvar_grid< T > const &other_grid) |
| Copy data from another grid of the same type, AND identical definition (boundaries, widths) Added for shared ABF. | |
| void | raw_data_out (T *out_data) const |
| Extract the grid data as they are represented in memory. Put the results in "out_data". | |
| void | raw_data_out (std::vector< T > &out_data) const |
| void | raw_data_in (const T *in_data) |
| Input the data as they are represented in memory. | |
| void | raw_data_in (const std::vector< T > &in_data) |
| size_t | raw_data_num () const |
| Size of the data as they are represented in memory. | |
| T const & | value (std::vector< int > const &ix, size_t const &imult=0) const |
| Get the binned value indexed by ix, or the first of them if the multiplicity is larger than 1. | |
| T const & | value (size_t i) const |
| Get the binned value indexed by linear address i. | |
| void | add_constant (T const &t) |
| Add a constant to all elements (fast loop) | |
| void | multiply_constant (cvm::real const &a) |
| Multiply all elements by a scalar constant (fast loop) | |
| void | remove_small_values (cvm::real const &a) |
| Assign values that are smaller than scalar constant the latter value (fast loop) | |
| std::vector< int > const | get_colvars_index (std::vector< colvarvalue > const &values) const |
| Get the bin indices corresponding to the provided values of the colvars. | |
| std::vector< int > const | get_colvars_index () const |
| Get the bin indices corresponding to the current values of the colvars. | |
| std::vector< int > const | get_colvars_index_bound () const |
| Get the bin indices corresponding to the provided values of the colvars and assign first or last bin if out of boundaries. | |
| cvm::real | bin_distance_from_boundaries (std::vector< colvarvalue > const &values, bool skip_hard_boundaries=false) |
| Get the minimal distance (in number of bins) from the boundaries; a negative number is returned if the given point is off-grid. | |
| void | map_grid (colvar_grid< T > const &other_grid) |
| Add data from another grid of the same type. More... | |
| void | add_grid (colvar_grid< T > const &other_grid, cvm::real scale_factor=1.0) |
| Add data from another grid of the same type, AND identical definition (boundaries, widths) | |
| virtual T | value_output (std::vector< int > const &ix, size_t const &imult=0) const |
| Return the value suitable for output purposes (so that it may be rescaled or manipulated without changing it permanently) More... | |
| virtual void | value_input (std::vector< int > const &ix, T const &t, size_t const &imult=0, bool add=false) |
| Get the value from a formatted output and transform it into the internal representation (the two may be different, e.g. when using colvar_grid_count) More... | |
| std::vector< int > const | new_index () const |
| Get the index corresponding to the "first" bin, to be used as the initial value for an index in looping. | |
| bool | index_ok (std::vector< int > const &ix) const |
| Check that the index is within range in each of the dimensions. | |
| void | incr (std::vector< int > &ix) const |
| Increment the index, in a way that will make it loop over the whole nd-dimensional array. | |
| std::string | get_state_params () const |
| Write the current grid parameters to a string. | |
| int | parse_params (std::string const &conf, colvarparse::Parse_Mode const parse_mode=colvarparse::parse_normal) |
| Read new grid parameters from a string. | |
| void | check_consistency () |
| Check that the grid information inside (boundaries, widths, ...) is consistent with the current setting of the colvars. | |
| void | check_consistency (colvar_grid< T > const &other_grid) |
| Check that the grid information inside (boundaries, widths, ...) is consistent with that of another grid. | |
| std::istream & | read_restart (std::istream &is) |
| Read all grid parameters and data from a formatted stream. | |
| cvm::memory_stream & | read_restart (cvm::memory_stream &is) |
| Read all grid parameters and data from an unformatted stream. | |
| std::ostream & | write_restart (std::ostream &os) |
| Write all grid parameters and data to a formatted stream. | |
| cvm::memory_stream & | write_restart (cvm::memory_stream &os) |
| Write all grid parameters and data to an unformatted stream. | |
| std::istream & | read_raw (std::istream &is) |
| Read all grid parameters and data from a formatted stream. | |
| cvm::memory_stream & | read_raw (cvm::memory_stream &is) |
| Read all grid parameters and data from an unformatted stream. | |
| std::ostream & | write_raw (std::ostream &os, size_t const buf_size=3) const |
| cvm::memory_stream & | write_raw (cvm::memory_stream &os, size_t const buf_size=3) const |
| std::istream & | read_multicol (std::istream &is, bool add=false) |
| Read a grid written by write_multicol(), incrementing if add is true. | |
| int | read_multicol (std::string const &filename, std::string description="grid file", bool add=false) |
| Read a grid written by write_multicol(), incrementing if add is true. | |
| std::ostream & | write_multicol (std::ostream &os) const |
| Write grid in a format which is both human-readable and gnuplot-friendly. | |
| int | write_multicol (std::string const &filename, std::string description="grid file") const |
| Write grid in a format which is both human-readable and gnuplot-friendly. | |
| std::ostream & | write_opendx (std::ostream &os) const |
| Write the grid data without labels, as they are represented in memory. | |
| int | write_opendx (std::string const &filename, std::string description="grid file") const |
| Write the grid data without labels, as they are represented in memory. | |
 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 ¶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... | |
Public Attributes | |
| size_t | nd |
| Number of dimensions. | |
| std::vector< int > | nx |
| Number of points along each dimension. | |
| std::vector< int > | nxc |
| Cumulative number of points along each dimension. | |
| size_t | mult |
| Multiplicity of each datum (allow the binning of non-scalar types such as atomic gradients) | |
| size_t | nt |
| Total number of grid points. | |
| std::vector< T > | data |
| Low-level array of values. | |
| std::vector< size_t > | new_data |
| Newly read data (used for count grids, when adding several grids read from disk) | |
| std::vector< colvar * > | cv |
| Colvars collected in this grid. | |
| std::vector< bool > | use_actual_value |
| Do we request actual value (for extended-system colvars)? | |
| std::vector< colvarvalue > | lower_boundaries |
| Lower boundaries of the colvars in this grid. | |
| std::vector< colvarvalue > | upper_boundaries |
| Upper boundaries of the colvars in this grid. | |
| std::vector< bool > | periodic |
| Whether some colvars are periodic. | |
| std::vector< bool > | hard_lower_boundaries |
| Whether some colvars have hard lower boundaries. | |
| std::vector< bool > | hard_upper_boundaries |
| Whether some colvars have hard upper boundaries. | |
| std::vector< cvm::real > | widths |
| Widths of the colvars in this grid. | |
| bool | has_parent_data |
| True if this is a count grid related to another grid of data. | |
| bool | has_data |
| Whether this grid has been filled with data or is still empty. | |
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... | |
| 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 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 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 ¶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. | |
| 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. | |
Detailed Description
template<class T>
class colvar_grid< T >
class colvar_grid< T >
Grid of values of a function of several collective variables.
- Parameters
-
T The data type
Only scalar colvars supported so far: vector colvars are treated as arrays
Constructor & Destructor Documentation
◆ colvar_grid() [1/2]
template<class T >
|
inline |
Constructor from explicit grid sizes.
- Parameters
-
nx_i Number of grid points along each dimension t Initial value for the function at each point (optional) mult_i Multiplicity of each value
◆ colvar_grid() [2/2]
template<class T >
|
inline |
Constructor from a vector of colvars.
- Parameters
-
add_extra_bin requests that non-periodic dimensions are extended by 1 bin to accommodate the integral (PMF) of another gridded quantity (gradient)
Member Function Documentation
◆ map_grid()
template<class T >
|
inline |
Add data from another grid of the same type.
Note: this function maps other_grid inside this one regardless of whether it fits or not.
◆ number_of_points()
template<class T >
|
inline |
Return the number of points in the i-th direction, if provided, or the total number
◆ value_input()
template<class T >
|
inlinevirtual |
Get the value from a formatted output and transform it into the internal representation (the two may be different, e.g. when using colvar_grid_count)
Reimplemented in colvar_grid_scalar, colvar_grid_gradient, and colvar_grid_count.
◆ value_output()
template<class T >
|
inlinevirtual |
Return the value suitable for output purposes (so that it may be rescaled or manipulated without changing it permanently)
Reimplemented in colvar_grid_scalar, and colvar_grid_gradient.
◆ wrap()
template<class T >
|
inline |
Wrap an index vector around periodic boundary conditions also checks validity of non-periodic indices
◆ wrap_detect_edge()
template<class T >
|
inline |
Wrap an index vector around periodic boundary conditions or detects edges if non-periodic
◆ wrap_to_edge()
template<class T >
|
inline |
Wrap an index vector around periodic boundary conditions or brings back to nearest edge if non-periodic
◆ write_raw() [1/2]
template<class T >
| cvm::memory_stream & colvar_grid< T >::write_raw | ( | cvm::memory_stream & | os, |
| size_t const | buf_size = 3 |
||
| ) | const |
Write all grid data to an unformatted stream
- Parameters
-
[in,out] os Stream object [in] buf_size Number of values per line (note: ignored because there is no formatting)
◆ write_raw() [2/2]
template<class T >
| std::ostream & colvar_grid< T >::write_raw | ( | std::ostream & | os, |
| size_t const | buf_size = 3 |
||
| ) | const |
Write all grid data to a formatted stream (without labels, as they are represented in memory)
- Parameters
-
[in,out] os Stream object [in] buf_size Number of values per line
The documentation for this class was generated from the following files:
