Integrate (1D, 2D or 3D) gradients. More...
#include <colvargrid.h>
Inheritance diagram for integrate_potential:
Collaboration diagram for integrate_potential:
Public Member Functions | |
| integrate_potential (std::vector< colvar * > &colvars, std::shared_ptr< colvar_grid_gradient > gradients) | |
| Constructor from a vector of colvars + gradient grid. | |
| integrate_potential (std::shared_ptr< colvar_grid_gradient > gradients) | |
| Constructor from a gradient grid (for processing grid files without a Colvars config) | |
| int | integrate (const int itmax, const cvm::real &tol, cvm::real &err, bool verbose=true) |
| Calculate potential from divergence (in 2D); return number of steps. | |
| void | update_div_neighbors (const std::vector< int > &ix) |
| Update matrix containing divergence and boundary conditions based on new gradient point value, in neighboring bins. | |
| void | update_div_local (const std::vector< int > &ix) |
| Update matrix containing divergence and boundary conditions called by update_div_neighbors and by colvarbias_abf::adiabatic_reweighting_update_gradient_pmf. | |
| void | set_div () |
| Set matrix containing divergence and boundary conditions based on complete gradient grid. | |
| void | set_zero_minimum () |
| Add constant to potential so that its minimum value is zero Useful e.g. for output. | |
 Public Member Functions inherited from colvar_grid_scalar | |
| colvar_grid_scalar () | |
| Default constructor. | |
| colvar_grid_scalar (colvar_grid_scalar const &g) | |
| Copy constructor (needed because of the grad pointer) | |
| virtual | ~colvar_grid_scalar () |
| Destructor. | |
| colvar_grid_scalar (std::vector< int > const &nx_i) | |
| Constructor from specific sizes arrays. | |
| colvar_grid_scalar (std::vector< colvar * > &colvars, bool add_extra_bin=false) | |
| Constructor from a vector of colvars. | |
| void | acc_value (std::vector< int > const &ix, cvm::real const &new_value, size_t const &imult=0) |
| Accumulate the value. | |
| 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. | |
| 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(), incrementin if data 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. | |
| void | vector_gradient_finite_diff (const std::vector< int > &ix0, std::vector< cvm::real > &grad) |
| Return the gradient of the scalar field from finite differences Input coordinates are those of gradient grid, shifted wrt scalar grid Should not be called on edges of scalar grid, provided the latter has margins wrt gradient grid. | |
| cvm::real | log_gradient_finite_diff (const std::vector< int > &ix0, int n=0, int offset=0) |
| Return the log-gradient from finite differences on the same grid for dimension n (colvar_grid_scalar) | |
| cvm::real | gradient_finite_diff (const std::vector< int > &ix0, int n=0) |
| Return the gradient of discrete count from finite differences on the same grid for dimension n (colvar_grid_scalar) | |
| virtual cvm::real | value_output (std::vector< int > const &ix, size_t const &imult=0) const override |
| Return the value of the function at ix divided by its number of samples (if the count grid is defined) More... | |
| virtual void | value_input (std::vector< int > const &ix, cvm::real const &new_value, size_t const &imult=0, bool add=false) override |
| Enter or add value but also deal with count grid. More... | |
| cvm::real | maximum_value () const |
| Return the highest value. | |
| cvm::real | minimum_value () const |
| Return the lowest value. | |
| cvm::real | minimum_pos_value () const |
| Return the lowest positive value. | |
| cvm::real | integral () const |
| Calculates the integral of the map (uses widths if they are defined) | |
| cvm::real | entropy () const |
| Assuming that the map is a normalized probability density, calculates the entropy (uses widths if they are defined) | |
| cvm::real | grid_rmsd (colvar_grid_scalar const &other_grid) const |
| Return the RMSD between this grid's data and another one Grids must have the same dimensions. | |
| Public Member Functions inherited from colvar_grid< cvm::real > | |
| 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, cvm::real const &t=cvm::real(), size_t const &mult_i=1) |
| Allocate data. | |
| int | setup () |
| Allocate data (allow initialization also after construction) | |
| void | reset (cvm::real const &t=cvm::real()) |
| Reset data (in case the grid is being reused) | |
| colvar_grid () | |
| Default constructor. | |
| colvar_grid (colvar_grid< cvm::real > 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, cvm::real const &t=cvm::real(), size_t mult_i=1) | |
| Constructor from explicit grid sizes. More... | |
| colvar_grid (std::vector< colvar * > const &colvars, cvm::real const &t=cvm::real(), size_t mult_i=1, bool add_extra_bin=false) | |
| Constructor from a vector of colvars. More... | |
| virtual | ~colvar_grid () |
| Destructor. | |
| 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_scalar (int const i, int const iv) const |
| Report the bin corresponding to the current value of item iv in 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 | 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. | |
| 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. | |
| 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. | |
| 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, cvm::real const &t, size_t const &imult=0) |
| Set the value at the point with index ix. | |
| void | set_value (size_t i, cvm::real const &t) |
| Set the value at the point with linear address i (for speed) | |
| cvm::real | get_value (size_t i) const |
| Get the value at the point with linear address i (for speed) | |
| void | delta_grid (colvar_grid< cvm::real > 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< cvm::real > 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 (cvm::real *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< cvm::real > &out_data) const |
| void | raw_data_in (const cvm::real *in_data) |
| Input the data as they are represented in memory. | |
| void | raw_data_in (const std::vector< cvm::real > &in_data) |
| size_t | raw_data_num () const |
| Size of the data as they are represented in memory. | |
| cvm::real 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. | |
| cvm::real const & | value (size_t i) const |
| Get the binned value indexed by linear address i. | |
| void | add_constant (cvm::real 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< cvm::real > const &other_grid) |
| Add data from another grid of the same type. More... | |
| void | add_grid (colvar_grid< cvm::real > const &other_grid, cvm::real scale_factor=1.0) |
| Add data from another grid of the same type, AND identical definition (boundaries, widths) | |
| virtual cvm::real | 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, cvm::real 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< cvm::real > 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 | |
| bool | b_smoothed |
| Flag requesting the use of a smoothed version of the gradient (default: false) | |
| Public Attributes inherited from colvar_grid_scalar | |
| colvar_grid_count * | samples |
| Provide the associated sample count by which each binned value should be divided. | |
| Public Attributes inherited from colvar_grid< cvm::real > | |
| 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< cvm::real > | 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. | |
Protected Member Functions | |
| void | get_grad (cvm::real *g, std::vector< int > &ix) |
| void | nr_linbcg_sym (const std::vector< cvm::real > &b, std::vector< cvm::real > &x, const cvm::real &tol, const int itmax, int &iter, cvm::real &err) |
| Solve linear system based on CG, valid for symmetric matrices only. | |
| cvm::real | l2norm (const std::vector< cvm::real > &x) |
| l2 norm of a vector | |
| void | atimes (const std::vector< cvm::real > &x, std::vector< cvm::real > &r) |
| Multiplication by sparse matrix representing Lagrangian (or its transpose) 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 ¶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 | |
| std::shared_ptr< colvar_grid_gradient > | gradients |
| std::vector< cvm::real > | divergence |
| Array holding divergence + boundary terms (modified Neumann) if not periodic. | |
| 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. | |
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. | |
Detailed Description
Integrate (1D, 2D or 3D) gradients.
Member Function Documentation
◆ atimes()
|
protected |
Multiplication by sparse matrix representing Lagrangian (or its transpose)
Multiplication by sparse matrix representing Laplacian NOTE: Laplacian must be symmetric for solving with CG
◆ get_grad()
|
protected |
Obtain the gradient vector at given location ix, if available or zero if it is on the edge of the gradient grid ix gets wrapped in PBC
The documentation for this class was generated from the following files:
- colvargrid.h
- colvargrid.cpp
