colvar_grid< T > Class Template Reference

Grid of values of a function of several collective variables. More...

#include <colvargrid.h>

Inheritance diagram for colvar_grid< T >:

List of all members.

Public Member Functions
size_t	number_of_colvars () const
	Return the number of colvars.
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	create (std::vector< int > const &nx_i, T const &t=T(), size_t const &mult_i=1)
	Allocate data (allow initialization also after construction).
void	create ()
	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; create() must be called after that;
	colvar_grid (std::vector< int > const &nx_i, T const &t=T(), size_t const &mult_i=1)
	Constructor from explicit grid sizes.
	colvar_grid (std::vector< colvar * > const &colvars, T const &t=T(), size_t const &mult_i=1, bool margin=false)
	Constructor from a vector of colvars.
void	wrap (std::vector< int > &ix) const
int	current_bin_scalar (int const i) const
	Report the bin corresponding to the current value of 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.
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.
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.
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).
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.
cvm::real	bin_distance_from_boundaries (std::vector< colvarvalue > const &values)
	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.
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)
	Return the value suitable for output purposes (so that it may be rescaled or manipulated without changing it permanently).
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).
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::ostream &	write_params (std::ostream &os)
	Write the grid parameters (number of colvars, boundaries, width and number of points).
bool	parse_params (std::string const &conf)
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 the one of another grid.
std::ostream &	write_raw (std::ostream &os, size_t const buf_size=3)
	Write the grid data without labels, as they are represented in memory.
std::istream &	read_raw (std::istream &is)
	Read data written by colvar_grid::write_raw().
void	read_raw_error ()
	To be called after colvar_grid::read_raw() returns an error.
void	write_multicol (std::ostream &os)
	Write the grid in a format which is both human readable and suitable for visualization e.g. with gnuplot.
std::istream &	read_multicol (std::istream &is, bool add=false)
	Read a grid written by colvar_grid::write_multicol() Adding data if add is true, replacing if false.
Public Attributes
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< 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
size_t	address (std::vector< int > const &ix) const
	Get the low-level index corresponding to an index.
Protected 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).
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.

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Detailed Description

template<class 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

Definition at line 19 of file colvargrid.h.

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Constructor & Destructor Documentation

template<class T> colvar_grid< T >::colvar_grid (   )  [inline]

Default constructor. Definition at line 154 of file colvargrid.h. : has_data (false) { save_delimiters = false; nd = nt = 0; }

template<class T> virtual colvar_grid< T >::~colvar_grid (   )  [inline, virtual]

Destructor. Definition at line 161 of file colvargrid.h. {}

template<class T> colvar_grid< T >::colvar_grid (  colvar_grid< T > const &  g  )  [inline]

"Almost copy-constructor": only copies configuration parameters from another grid, but doesn't reallocate stuff; create() must be called after that; Definition at line 167 of file colvargrid.h. : has_data (false), nd (g.nd), mult (g.mult), cv (g.cv), lower_boundaries (g.lower_boundaries), upper_boundaries (g.upper_boundaries), periodic (g.periodic), widths (g.widths), data() { save_delimiters = false; }

template<class T> colvar_grid< T >::colvar_grid (  std::vector< int > const &  nx_i, T const &  t = T(), size_t const &  mult_i = 1 )  [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 Definition at line 184 of file colvargrid.h. : has_data (false) { save_delimiters = false; this->create (nx_i, t, mult_i); }

template<class T> colvar_grid< T >::colvar_grid (  std::vector< colvar * > const &  colvars, T const &  t = T(), size_t const &  mult_i = 1, bool  margin = false )  [inline]

Constructor from a vector of colvars. Definition at line 193 of file colvargrid.h. : cv (colvars), has_data (false) { save_delimiters = false; std::vector<int> nx_i; if (cvm::debug()) cvm::log ("Allocating a grid for "+cvm::to_str (colvars.size())+ " collective variables.\n"); for (size_t i = 0; i < cv.size(); i++) { if (cv[i]->type() != colvarvalue::type_scalar) { cvm::fatal_error ("Colvar grids can only be automatically " "constructed for scalar variables. " "ABF and histogram can not be used; metadynamics " "can be used with useGrids disabled.\n"); } if (cv[i]->width <= 0.0) { cvm::fatal_error ("Tried to initialize a grid on a " "variable with negative or zero width.\n"); } if (!cv[i]->tasks[colvar::task_lower_boundary] || !cv[i]->tasks[colvar::task_upper_boundary]) { cvm::fatal_error ("Tried to initialize a grid on a " "variable with undefined boundaries.\n"); } widths.push_back (cv[i]->width); periodic.push_back (cv[i]->periodic_boundaries()); if (margin) { if (periodic[i]) { // Shift the grid by half the bin width (values at edges instead of center of bins) lower_boundaries.push_back (cv[i]->lower_boundary.real_value - 0.5 * widths[i]); upper_boundaries.push_back (cv[i]->upper_boundary.real_value - 0.5 * widths[i]); } else { // Make this grid larger by one bin width lower_boundaries.push_back (cv[i]->lower_boundary.real_value - 0.5 * widths[i]); upper_boundaries.push_back (cv[i]->upper_boundary.real_value + 0.5 * widths[i]); } } else { lower_boundaries.push_back (cv[i]->lower_boundary); upper_boundaries.push_back (cv[i]->upper_boundary); } { cvm::real nbins = ( upper_boundaries[i].real_value - lower_boundaries[i].real_value ) / widths[i]; int nbins_round = (int)(nbins+0.5); if (std::fabs (nbins - cvm::real (nbins_round)) > 1.0E-10) { cvm::log ("Warning: grid interval ("+ cvm::to_str (lower_boundaries[i], cvm::cv_width, cvm::cv_prec)+" - "+ cvm::to_str (upper_boundaries[i], cvm::cv_width, cvm::cv_prec)+ ") is not commensurate to its bin width ("+ cvm::to_str (widths[i], cvm::cv_width, cvm::cv_prec)+").\n"); upper_boundaries[i].real_value = lower_boundaries[i].real_value + (nbins_round * widths[i]); } if (cvm::debug()) cvm::log ("Number of points is "+cvm::to_str ((int) nbins_round)+ " for the colvar no. "+cvm::to_str (i+1)+".\n"); nx_i.push_back (nbins_round); } } create (nx_i, t, mult_i); }

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Member Function Documentation

template<class T> void colvar_grid< T >::add_constant (  T const &  t  )  [inline]

Add a constant to all elements (fast loop). Definition at line 344 of file colvargrid.h. Referenced by colvarbias_meta::write_pmf(). { for (size_t i = 0; i < nt; i++) data[i] += t; has_data = true; }

template<class T> void colvar_grid< T >::add_grid (  colvar_grid< T > const &  other_grid, cvm::real  scale_factor = 1.0 )  [inline]

Add data from another grid of the same type, AND identical definition (boundaries, widths). Definition at line 454 of file colvargrid.h. Referenced by colvarbias_meta::write_pmf(). { if (other_grid.multiplicity() != this->multiplicity()) cvm::fatal_error ("Error: trying to sum togetehr two grids with values of " "different multiplicity.\n"); if (scale_factor != 1.0) for (size_t i = 0; i < data.size(); i++) { data[i] += scale_factor * other_grid.data[i]; } else // skip multiplication if possible for (size_t i = 0; i < data.size(); i++) { data[i] += other_grid.data[i]; } has_data = true; }

template<class T> size_t colvar_grid< T >::address (  std::vector< int > const &  ix  )  const [inline, protected]

Get the low-level index corresponding to an index. Definition at line 49 of file colvargrid.h. Referenced by colvar_grid< size_t >::set_value(), colvar_grid< size_t >::value(), and colvar_grid< size_t >::value_input(). { size_t addr = 0; for (size_t i = 0; i < nd; i++) { addr += ix[i]*nxc[i]; if (cvm::debug()) { if (ix[i] >= nx[i]) cvm::fatal_error ("Error: exceeding bounds in colvar_grid.\n"); } } return addr; }

template<class T> cvm::real colvar_grid< T >::bin_distance_from_boundaries (  std::vector< colvarvalue > const &  values  )  [inline]

Get the minimal distance (in number of bins) from the boundaries; a negative number is returned if the given point is off-grid. Definition at line 384 of file colvargrid.h. Referenced by colvarbias_meta::create_hill(), colvarbias_meta::read_hill(), and colvarbias_meta::recount_hills_off_grid(). { cvm::real minimum = 1.0E+16; for (size_t i = 0; i < nd; i++) { if (periodic[i]) continue; cvm::real dl = std::sqrt (cv[i]->dist2 (values[i], lower_boundaries[i])) / widths[i]; cvm::real du = std::sqrt (cv[i]->dist2 (values[i], upper_boundaries[i])) / widths[i]; if (values[i].real_value < lower_boundaries[i]) dl *= -1.0; if (values[i].real_value > upper_boundaries[i]) du *= -1.0; if (dl < minimum) minimum = dl; if (du < minimum) minimum = du; } return minimum; }

template<class T> colvarvalue colvar_grid< T >::bin_to_value_scalar (  int const &  i_bin, colvarvalue const &  new_offset, cvm::real const &  new_width )  const [inline]

Same as the standard version, but uses different parameters. Definition at line 317 of file colvargrid.h. { return new_offset.real_value + new_width * (0.5 + i_bin); }

template<class T> colvarvalue colvar_grid< T >::bin_to_value_scalar (  int const &  i_bin, int const   i )  const [inline]

Use the two boundaries and the width to report the central value corresponding to a bin index. Definition at line 311 of file colvargrid.h. Referenced by colvarbias_meta::project_hills(), and colvar_grid< size_t >::write_multicol(). { return lower_boundaries[i].real_value + widths[i] * (0.5 + i_bin); }

template<class T> void colvar_grid< T >::check_consistency (  colvar_grid< T > const &  other_grid  )  [inline]

Check that the grid information inside (boundaries, widths, ...) is consistent with the one of another grid. Definition at line 640 of file colvargrid.h. { for (size_t i = 0; i < nd; i++) { // we skip dist2(), because periodicities and the like should // matter: boundaries should be EXACTLY the same (otherwise, // map_grid() should be used) if ( (std::fabs (other_grid.lower_boundaries[i] - lower_boundaries[i]) > 1.0E-10) || (std::fabs (other_grid.upper_boundaries[i] - upper_boundaries[i]) > 1.0E-10) || (std::fabs (other_grid.widths[i] - widths[i]) > 1.0E-10) || (data.size() != other_grid.data.size()) ) { cvm::fatal_error ("Error: inconsistency between " "two grids that are supposed to be equal, " "aside from the data stored.\n"); } } }

template<class T> void colvar_grid< T >::check_consistency (   )  [inline]

Check that the grid information inside (boundaries, widths, ...) is consistent with the current setting of the colvars. Definition at line 622 of file colvargrid.h. { for (size_t i = 0; i < nd; i++) { if ( (std::sqrt (cv[i]->dist2 (cv[i]->lower_boundary, lower_boundaries[i])) > 1.0E-10) || (std::sqrt (cv[i]->dist2 (cv[i]->upper_boundary, upper_boundaries[i])) > 1.0E-10) || (std::sqrt (cv[i]->dist2 (cv[i]->width, widths[i])) > 1.0E-10) ) { cvm::fatal_error ("Error: restart information for a grid is " "inconsistent with that of its colvars.\n"); } } }

template<class T> void colvar_grid< T >::create (   )  [inline]

Allocate data (allow initialization also after construction). Definition at line 141 of file colvargrid.h. Referenced by colvar_grid< size_t >::colvar_grid(), colvar_grid< size_t >::create(), and colvar_grid< size_t >::parse_params(). { create (this->nx, T(), this->mult); }

template<class T> void colvar_grid< T >::create (  std::vector< int > const &  nx_i, T const &  t = T(), size_t const &  mult_i = 1 )  [inline]

Allocate data (allow initialization also after construction). Definition at line 118 of file colvargrid.h. Referenced by colvarbias_meta::update(). { mult = mult_i; nd = nx_i.size(); nxc.resize (nd); nx = nx_i; nt = mult; for (int i = nd-1; i >= 0; i--) { if (nx_i[i] <= 0) cvm::fatal_error ("Error: providing an invalid number of points, "+ cvm::to_str (nx_i[i])+".\n"); nxc[i] = nt; nt *= nx[i]; } data.reserve (nt); data.assign (nt, t); }

template<class T> int colvar_grid< T >::current_bin_scalar (  int const   i  )  const [inline]

Report the bin corresponding to the current value of variable i. Definition at line 289 of file colvargrid.h. Referenced by colvar_grid< size_t >::get_colvars_index(), colvarbias_histogram::update(), and colvarbias_abf::update(). { return value_to_bin_scalar (cv[i]->value(), i); }

template<class T> std::vector<int> const colvar_grid< T >::get_colvars_index (   )  const [inline]

Get the bin indices corresponding to the current values of the colvars. Definition at line 372 of file colvargrid.h. { std::vector<int> index = new_index(); for (size_t i = 0; i < nd; i++) { index[i] = current_bin_scalar (i); } return index; }

template<class T> std::vector<int> const colvar_grid< T >::get_colvars_index (  std::vector< colvarvalue > const &  values  )  const [inline]

Get the bin indices corresponding to the provided values of the colvars. Definition at line 361 of file colvargrid.h. Referenced by colvarbias_meta::update(). { std::vector<int> index = new_index(); for (size_t i = 0; i < nd; i++) { index[i] = value_to_bin_scalar (values[i], i); } return index; }

template<class T> void colvar_grid< T >::incr (  std::vector< int > &  ix  )  const [inline]

Increment the index, in a way that will make it loop over the whole nd-dimensional array. Definition at line 521 of file colvargrid.h. Referenced by colvar_grid< size_t >::map_grid(), colvarbias_meta::project_hills(), colvar_grid< size_t >::read_multicol(), colvar_grid< size_t >::read_raw(), colvar_grid< size_t >::write_multicol(), and colvar_grid< size_t >::write_raw(). { for (int i = ix.size()-1; i >= 0; i--) { ix[i]++; if (ix[i] >= nx[i]) { if (i > 0) { ix[i] = 0; continue; } else { // this is the last iteration, a non-valid index is being // set for the outer index, which will be caught by // index_ok() ix[0] = nx[0]; return; } } else { return; } } }

template<class T> bool colvar_grid< T >::index_ok (  std::vector< int > const &  ix  )  const [inline]

Check that the index is within range in each of the dimensions. Definition at line 510 of file colvargrid.h. Referenced by colvar_grid< size_t >::map_grid(), colvarbias_meta::project_hills(), colvar_grid< size_t >::read_multicol(), colvar_grid< size_t >::read_raw(), colvarbias_meta::update(), colvarbias_histogram::update(), colvarbias_abf::update(), colvar_grid< size_t >::write_multicol(), and colvar_grid< size_t >::write_raw(). { for (size_t i = 0; i < nd; i++) { if ( (ix[i] < 0) || (ix[i] >= int (nx[i])) ) return false; } return true; }

template<class T> void colvar_grid< T >::map_grid (  colvar_grid< T > const &  other_grid  )  [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. Definition at line 413 of file colvargrid.h. Referenced by colvarbias_meta::read_restart(), and colvarbias_meta::update(). { if (other_grid.multiplicity() != this->multiplicity()) cvm::fatal_error ("Error: trying to merge two grids with values of " "different multiplicity.\n"); std::vector<colvarvalue> const &gb = this->lower_boundaries; std::vector<cvm::real> const &gw = this->widths; std::vector<colvarvalue> const &ogb = other_grid.lower_boundaries; std::vector<cvm::real> const &ogw = other_grid.widths; std::vector<int> ix = this->new_index(); std::vector<int> oix = other_grid.new_index(); if (cvm::debug()) cvm::log ("Remapping grid...\n"); for ( ; this->index_ok (ix); this->incr (ix)) { for (size_t i = 0; i < nd; i++) { oix[i] = value_to_bin_scalar (bin_to_value_scalar (ix[i], gb[i], gw[i]), ogb[i], ogw[i]); } if (! other_grid.index_ok (oix)) { continue; } for (size_t im = 0; im < mult; im++) { this->set_value (ix, other_grid.value (oix, im), im); } } has_data = true; if (cvm::debug()) cvm::log ("Remapping done.\n"); }

template<class T> size_t colvar_grid< T >::multiplicity (   )  const [inline]

Return the multiplicity of the type used. Definition at line 112 of file colvargrid.h. Referenced by colvar_grid< size_t >::add_grid(), and colvar_grid< size_t >::map_grid(). { return mult; }

template<class T> void colvar_grid< T >::multiply_constant (  cvm::real const &  a  )  [inline]

Multiply all elements by a scalar constant (fast loop). Definition at line 352 of file colvargrid.h. Referenced by colvarbias_meta::write_pmf(). { for (size_t i = 0; i < nt; i++) data[i] *= a; }

template<class T> std::vector<int> const colvar_grid< T >::new_index (   )  const [inline]

Get the index corresponding to the "first" bin, to be used as the initial value for an index in looping. Definition at line 503 of file colvargrid.h. Referenced by colvar_grid< size_t >::get_colvars_index(), colvar_grid< size_t >::map_grid(), colvarbias_meta::project_hills(), colvar_grid< size_t >::read_multicol(), colvar_grid< size_t >::read_raw(), colvar_grid< size_t >::write_multicol(), and colvar_grid< size_t >::write_raw(). { return std::vector<int> (nd, 0); }

template<class T> size_t colvar_grid< T >::number_of_colvars (   )  const [inline]

Return the number of colvars. Definition at line 83 of file colvargrid.h. { return nd; }

template<class T> size_t colvar_grid< T >::number_of_points (  int const   icv = -1  )  const [inline]

Return the number of points in the i-th direction, if provided, or the total number Definition at line 90 of file colvargrid.h. { if (icv < 0) { return nt; } else { return nx[icv]; } }

template<class T> bool colvar_grid< T >::parse_params (  std::string const &  conf  )  [inline]

Definition at line 575 of file colvargrid.h. { std::vector<int> old_nx = nx; std::vector<colvarvalue> old_lb = lower_boundaries; { size_t nd_in = 0; colvarparse::get_keyval (conf, "n_colvars", nd_in, nd, colvarparse::parse_silent); if (nd_in != nd) cvm::fatal_error ("Error: trying to read data for a grid " "that contains a different number of colvars ("+ cvm::to_str (nd_in)+") than the grid defined " "in the configuration file ("+cvm::to_str (nd)+ ").\n"); } colvarparse::get_keyval (conf, "lower_boundaries", lower_boundaries, lower_boundaries, colvarparse::parse_silent); colvarparse::get_keyval (conf, "upper_boundaries", upper_boundaries, upper_boundaries, colvarparse::parse_silent); colvarparse::get_keyval (conf, "widths", widths, widths, colvarparse::parse_silent); colvarparse::get_keyval (conf, "sizes", nx, nx, colvarparse::parse_silent); bool new_params = false; for (size_t i = 0; i < nd; i++) { if ( (old_nx[i] != nx[i]) || (std::sqrt (cv[i]->dist2 (old_lb[i], lower_boundaries[i])) > 1.0E-10) ) { new_params = true; } } // reallocate the array in case the grid params have just changed if (new_params) { data.resize (0); this->create (nx, T(), mult); } return true; }

template<class T> std::istream& colvar_grid< T >::read_multicol (  std::istream &  is, bool  add = false )  [inline]

Read a grid written by colvar_grid::write_multicol() Adding data if add is true, replacing if false. Definition at line 760 of file colvargrid.h. { // Data in the header: nColvars, then for each // xiMin, dXi, nPoints, periodic std::string hash; cvm::real lower, width, x; size_t n, periodic; bool remap; std::vector<T> new_value; std::vector<int> nx_read; std::vector<int> bin; if ( cv.size() != nd ) { cvm::fatal_error ("Cannot read grid file: missing reference to colvars."); } if ( !(is >> hash) || (hash != "#") ) { cvm::fatal_error ("Error reading grid at position "+ cvm::to_str (is.tellg())+" in stream (read \"" + hash + "\")\n"); } is >> n; if ( n != nd ) { cvm::fatal_error ("Error reading grid: wrong number of collective variables.\n"); } nx_read.resize (n); bin.resize (n); new_value.resize (mult); if (this->has_parent_data && add) { new_data.resize (data.size()); } remap = false; for (size_t i = 0; i < nd; i++ ) { if ( !(is >> hash) || (hash != "#") ) { cvm::fatal_error ("Error reading grid at position "+ cvm::to_str (is.tellg())+" in stream (read \"" + hash + "\")\n"); } is >> lower >> width >> nx_read[i] >> periodic; if ( (std::fabs (lower - lower_boundaries[i].real_value) > 1.0e-10) || (std::fabs (width - widths[i] ) > 1.0e-10) || (nx_read[i] != nx[i]) ) { cvm::log ("Warning: reading from different grid definition (colvar " + cvm::to_str (i+1) + "); remapping data on new grid.\n"); remap = true; } } if ( remap ) { // re-grid data while (is.good()) { bool end_of_file = false; for (size_t i = 0; i < nd; i++ ) { if ( !(is >> x) ) end_of_file = true; bin[i] = value_to_bin_scalar (x, i); } if (end_of_file) break; for (size_t imult = 0; imult < mult; imult++) { is >> new_value[imult]; } if ( index_ok(bin) ) { for (size_t imult = 0; imult < mult; imult++) { value_input (bin, new_value[imult], imult, add); } } } } else { // do not re-grid the data but assume the same grid is used for (std::vector<int> ix = new_index(); index_ok (ix); incr (ix) ) { for (size_t i = 0; i < nd; i++ ) { is >> x; } for (size_t imult = 0; imult < mult; imult++) { is >> new_value[imult]; value_input (ix, new_value[imult], imult, add); } } } has_data = true; return is; }

template<class T> std::istream& colvar_grid< T >::read_raw (  std::istream &  is  )  [inline]

Read data written by colvar_grid::write_raw(). Definition at line 689 of file colvargrid.h. { size_t const start_pos = is.tellg(); for (std::vector<int> ix = new_index(); index_ok (ix); incr (ix)) { for (size_t imult = 0; imult < mult; imult++) { T new_value; if (is >> new_value) { value_input (ix, new_value, imult); } else { is.clear(); is.seekg (start_pos, std::ios::beg); is.setstate (std::ios::failbit); return is; } } } has_data = true; return is; }

template<class T> void colvar_grid< T >::read_raw_error (   )  [inline]

To be called after colvar_grid::read_raw() returns an error. Definition at line 712 of file colvargrid.h. { cvm::fatal_error ("Error: failed to read all of the grid points from file. Possible explanations: grid parameters in the configuration (lowerBoundary, upperBoundary, width) are different from those in the file, or the file is corrupt/incomplete.\n"); }

template<class T> void colvar_grid< T >::reset (  T const &  t = T()  )  [inline]

Reset data (in case the grid is being reused). Definition at line 147 of file colvargrid.h. Referenced by colvarbias_meta::project_hills(), colvarbias_meta::update(), colvarbias_abf::update(), and colvarbias_meta::write_pmf(). { data.assign (nt, t); }

template<class T> void colvar_grid< T >::set_sizes (  std::vector< int > const &  new_sizes  )  [inline]

Set the sizes in each direction. Definition at line 106 of file colvargrid.h. { nx = new_sizes; }

template<class T> void colvar_grid< T >::set_value (  std::vector< int > const &  ix, T const &  t, size_t const &  imult = 0 )  [inline]

Set the value at the point with index ix. Definition at line 325 of file colvargrid.h. Referenced by colvar_grid< size_t >::map_grid(). { data[this->address (ix)+imult] = t; has_data = true; }

template<class T> std::vector<int> const& colvar_grid< T >::sizes (   )  const [inline]

Get the sizes in each direction. Definition at line 100 of file colvargrid.h. Referenced by colvarbias_meta::update(). { return nx; }

template<class T> T const& colvar_grid< T >::value (  std::vector< int > const &  ix, size_t const &  imult = 0 )  const [inline]

Get the binned value indexed by ix, or the first of them if the multiplicity is larger than 1. Definition at line 336 of file colvargrid.h. Referenced by colvar_grid_gradient::average(), colvarbias_meta::calc_hills(), colvar_grid< size_t >::current_bin_scalar(), colvar_grid< size_t >::map_grid(), colvarbias_meta::update(), colvarbias_abf::update(), colvar_grid_gradient::value_input(), colvar_grid_scalar::value_input(), colvar_grid_gradient::value_output(), colvar_grid_scalar::value_output(), colvar_grid< size_t >::value_output(), and colvar_grid_gradient::write_1D_integral(). { return data[this->address (ix) + imult]; }

template<class T> virtual void colvar_grid< T >::value_input (  std::vector< int > const &  ix, T const &  t, size_t const &  imult = 0, bool  add = false )  [inline, virtual]

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_count, colvar_grid_scalar, and colvar_grid_gradient. Definition at line 483 of file colvargrid.h. Referenced by colvar_grid< size_t >::read_multicol(), and colvar_grid< size_t >::read_raw(). { if ( add ) data[address (ix) + imult] += t; else data[address (ix) + imult] = t; has_data = true; }

template<class T> virtual T colvar_grid< T >::value_output (  std::vector< int > const &  ix, size_t const &  imult = 0 )  [inline, virtual]

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. Definition at line 474 of file colvargrid.h. Referenced by colvar_grid< size_t >::write_multicol(), and colvar_grid< size_t >::write_raw(). { return value (ix, imult); }

template<class T> int colvar_grid< T >::value_to_bin_scalar (  colvarvalue const &  value, colvarvalue const &  new_offset, cvm::real const &  new_width )  const [inline]

Same as the standard version, but uses another grid definition. Definition at line 302 of file colvargrid.h. { return (int) std::floor ( (value.real_value - new_offset.real_value) / new_width ); }

template<class T> int colvar_grid< T >::value_to_bin_scalar (  colvarvalue const &  value, const int  i )  const [inline]

Use the lower boundary and the width to report which bin the provided value is in. Definition at line 296 of file colvargrid.h. Referenced by colvar_grid< size_t >::current_bin_scalar(), colvar_grid< size_t >::get_colvars_index(), colvar_grid< size_t >::map_grid(), and colvar_grid< size_t >::read_multicol(). { return (int) std::floor ( (value.real_value - lower_boundaries[i].real_value) / widths[i] ); }

template<class T> void colvar_grid< T >::wrap (  std::vector< int > &  ix  )  const [inline]

Wrap an index vector around periodic boundary conditions also checks validity of non-periodic indices Definition at line 275 of file colvargrid.h. { for (size_t i = 0; i < nd; i++) { if (periodic[i]) { ix[i] = (ix[i] + nx[i]) % nx[i]; //to ensure non-negative result } else { if (ix[i] < 0 || ix[i] >= nx[i]) cvm::fatal_error ("Trying to wrap illegal index vector (non-PBC): " + cvm::to_str (ix)); } } }

template<class T> void colvar_grid< T >::write_multicol (  std::ostream &  os  )  [inline]

Write the grid in a format which is both human readable and suitable for visualization e.g. with gnuplot. Definition at line 719 of file colvargrid.h. Referenced by colvarbias_histogram::update(), and colvarbias_meta::write_pmf(). { std::streamsize const w = os.width(); std::streamsize const p = os.precision(); // Data in the header: nColvars, then for each // xiMin, dXi, nPoints, periodic os << std::setw (2) << "# " << nd << "\n"; for (size_t i = 0; i < nd; i++) { os << "# " << std::setw (10) << lower_boundaries[i] << std::setw (10) << widths[i] << std::setw (10) << nx[i] << " " << periodic[i] << "\n"; } for (std::vector<int> ix = new_index(); index_ok (ix); incr (ix) ) { if (ix.back() == 0) { // if the last index is 0, add a new line to mark the new record os << "\n"; } for (size_t i = 0; i < nd; i++) { os << " " << std::setw (w) << std::setprecision (p) << bin_to_value_scalar (ix[i], i); } os << " "; for (size_t imult = 0; imult < mult; imult++) { os << " " << std::setw (w) << std::setprecision (p) << value_output (ix, imult); } os << "\n"; } }

template<class T> std::ostream& colvar_grid< T >::write_params (  std::ostream &  os  )  [inline]

Write the grid parameters (number of colvars, boundaries, width and number of points). Definition at line 546 of file colvargrid.h. { os << "grid_parameters {\n n_colvars " << nd << "\n"; os << " lower_boundaries "; for (size_t i = 0; i < nd; i++) os << " " << lower_boundaries[i]; os << "\n"; os << " upper_boundaries "; for (size_t i = 0; i < nd; i++) os << " " << upper_boundaries[i]; os << "\n"; os << " widths "; for (size_t i = 0; i < nd; i++) os << " " << widths[i]; os << "\n"; os << " sizes "; for (size_t i = 0; i < nd; i++) os << " " << nx[i]; os << "\n"; os << "}\n"; return os; }

template<class T> std::ostream& colvar_grid< T >::write_raw (  std::ostream &  os, size_t const   buf_size = 3 )  [inline]

Write the grid data without labels, as they are represented in memory. Parameters: buf_size  Number of values per line Definition at line 664 of file colvargrid.h. { std::streamsize const w = os.width(); std::streamsize const p = os.precision(); std::vector<int> ix = new_index(); size_t count = 0; for ( ; index_ok (ix); incr (ix)) { for (size_t imult = 0; imult < mult; imult++) { os << " " << std::setw (w) << std::setprecision (p) << value_output (ix, imult); if (((++count) % buf_size) == 0) os << "\n"; } } // write a final newline only if buffer is not empty if ((count % buf_size) != 0) os << "\n"; return os; }

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Member Data Documentation

template<class T> std::vector<colvar *> colvar_grid< T >::cv [protected]

Colvars collected in this grid. Definition at line 46 of file colvargrid.h.

template<class T> std::vector<T> colvar_grid< T >::data [protected]

Low-level array of values. Definition at line 40 of file colvargrid.h. Referenced by colvar_grid< size_t >::add_grid(), and colvar_grid< size_t >::check_consistency().

template<class T> bool colvar_grid< T >::has_data

Whether this grid has been filled with data or is still empty. Definition at line 80 of file colvargrid.h.

template<class T> bool colvar_grid< T >::has_parent_data

True if this is a count grid related to another grid of data. Definition at line 77 of file colvargrid.h. Referenced by colvarbias_abf::colvarbias_abf().

template<class T> std::vector<colvarvalue> colvar_grid< T >::lower_boundaries

Lower boundaries of the colvars in this grid. Definition at line 65 of file colvargrid.h. Referenced by colvar_grid< size_t >::check_consistency(), colvar_grid< size_t >::map_grid(), and colvarbias_meta::update().

template<class T> size_t colvar_grid< T >::mult [protected]

Multiplicity of each datum (allow the binning of non-scalar types). Definition at line 34 of file colvargrid.h.

template<class T> size_t colvar_grid< T >::nd [protected]

Number of dimensions. Definition at line 24 of file colvargrid.h.

template<class T> std::vector<size_t> colvar_grid< T >::new_data [protected]

Newly read data (used for count grids, when adding several grids read from disk). Definition at line 43 of file colvargrid.h.

template<class T> size_t colvar_grid< T >::nt [protected]

Total number of grid points. Definition at line 37 of file colvargrid.h.

template<class T> std::vector<int> colvar_grid< T >::nx [protected]

Number of points along each dimension. Definition at line 27 of file colvargrid.h.

template<class T> std::vector<int> colvar_grid< T >::nxc [protected]

Cumulative number of points along each dimension. Definition at line 30 of file colvargrid.h.

template<class T> std::vector<bool> colvar_grid< T >::periodic

Whether some colvars are periodic. Definition at line 71 of file colvargrid.h.

template<class T> std::vector<colvarvalue> colvar_grid< T >::upper_boundaries

Upper boundaries of the colvars in this grid. Definition at line 68 of file colvargrid.h. Referenced by colvar_grid< size_t >::check_consistency(), and colvarbias_meta::update().

template<class T> std::vector<cvm::real> colvar_grid< T >::widths

Widths of the colvars in this grid. Definition at line 74 of file colvargrid.h. Referenced by colvarbias_meta::calc_hills(), colvar_grid< size_t >::check_consistency(), and colvar_grid< size_t >::map_grid().

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

• colvargrid.h

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