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colvar_grid_gradient Class Reference

Class for accumulating the gradient of a scalar function on a grid. More...

#include <colvargrid.h>

Inheritance diagram for colvar_grid_gradient:

colvar_grid< cvm::real > colvarparse List of all members.

Public Member Functions

 colvar_grid_gradient ()
 Default constructor.
virtual ~colvar_grid_gradient ()
 Destructor.
 colvar_grid_gradient (std::vector< int > const &nx_i)
 Constructor from specific sizes arrays.
 colvar_grid_gradient (std::vector< colvar * > &colvars)
 Constructor from a vector of colvars.
void acc_grad (std::vector< int > const &ix, cvm::real const *grads)
 Accumulate the gradient.
void acc_force (std::vector< int > const &ix, cvm::real const *forces)
 Accumulate the gradient based on the force (i.e. sums the opposite of the force).
virtual cvm::real value_output (std::vector< int > const &ix, size_t const &imult=0)
 Return the value of the function at ix divided by its number of samples (if the count grid is defined).
virtual void value_input (std::vector< int > const &ix, cvm::real const &new_value, size_t const &imult=0, bool add=false)
 Get the value from a formatted output and transform it into the internal representation (it may have been rescaled or manipulated).
std::istream & read_restart (std::istream &is)
 Read the grid from a restart.
std::ostream & write_restart (std::ostream &os)
 Write the grid to a restart.
cvm::real average ()
 Compute and return average value for a 1D gradient grid.
void write_1D_integral (std::ostream &os)
 If the grid is 1-dimensional, integrate it and write the integral to a file.

Public Attributes

colvar_grid_count * samples
 Provide the sample count by which each binned value should be divided.

Detailed Description

Class for accumulating the gradient of a scalar function on a grid.

Definition at line 1049 of file colvargrid.h.

Constructor & Destructor Documentation

colvar_grid_gradient::colvar_grid_gradient (   ) 
 

Default constructor.

Definition at line 105 of file colvargrid.C.

References cvm.

00106   : colvar_grid<cvm::real>(), samples (NULL)
00107 {}

virtual colvar_grid_gradient::~colvar_grid_gradient (   )  [inline, virtual]
 

Destructor.

Definition at line 1061 of file colvargrid.h.

01062   {}

colvar_grid_gradient::colvar_grid_gradient (  std::vector< int > const &  nx_i  ) 
 

Constructor from specific sizes arrays.

Definition at line 109 of file colvargrid.C.

References cvm.

00110   : colvar_grid<cvm::real> (nx_i, 0.0, nx_i.size()), samples (NULL)
00111 {}

colvar_grid_gradient::colvar_grid_gradient (  std::vector< colvar * > &  colvars  ) 
 

Constructor from a vector of colvars.

Definition at line 113 of file colvargrid.C.

References cvm.

00114   : colvar_grid<cvm::real> (colvars, 0.0, colvars.size()), samples (NULL)
00115 {}

Member Function Documentation

void colvar_grid_gradient::acc_force (  std::vector< int > const &  ix,
cvm::real const *  forces
)  [inline]
 

Accumulate the gradient based on the force (i.e. sums the opposite of the force).

Definition at line 1081 of file colvargrid.h.

References colvar_grid< cvm::real >::address(), colvar_grid_count::incr_count(), and samples.

Referenced by colvarbias_meta::project_hills(), and colvarbias_abf::update().

01081                                                                           {
01082     for (size_t imult = 0; imult < mult; imult++) {
01083       data[address (ix) + imult] -= forces[imult];
01084     }
01085     if (samples)
01086       samples->incr_count (ix);
01087   }

void colvar_grid_gradient::acc_grad (  std::vector< int > const &  ix,
cvm::real const *  grads
)  [inline]
 

Accumulate the gradient.

Definition at line 1071 of file colvargrid.h.

References colvar_grid< cvm::real >::address(), colvar_grid_count::incr_count(), and samples.

01071                                                                         {
01072     for (size_t imult = 0; imult < mult; imult++) {
01073       data[address (ix) + imult] += grads[imult];
01074     }
01075     if (samples)
01076       samples->incr_count (ix);
01077   }

cvm::real colvar_grid_gradient::average (   )  [inline]
 

Compute and return average value for a 1D gradient grid.

Definition at line 1132 of file colvargrid.h.

References colvar_grid< cvm::real >::incr(), colvar_grid< cvm::real >::index_ok(), colvar_grid< cvm::real >::new_index(), colvarmodule::real, samples, colvar_grid< cvm::real >::value(), and colvar_grid< T >::value().

Referenced by colvarbias_abf::update(), and write_1D_integral().

01133   {
01134     size_t n = 0;
01135 
01136     if (nd != 1 || nx[0] == 0) {
01137       return 0.0;
01138     }
01139 
01140     cvm::real sum = 0.0;
01141     std::vector<int> ix = new_index();
01142     if (samples) {
01143       for ( ; index_ok (ix); incr (ix)) {
01144         if ( (n = samples->value (ix)) )
01145           sum += value (ix) / n;
01146       }
01147     } else {
01148       for ( ; index_ok (ix); incr (ix)) {
01149         sum += value (ix);
01150       }
01151     }
01152     return (sum / cvm::real (nx[0]));
01153   }

std::istream & colvar_grid_gradient::read_restart (  std::istream &  is  ) 
 

Read the grid from a restart.

Definition at line 117 of file colvargrid.C.

References colvarmodule::log(), colvar_grid< cvm::real >::parse_params(), and colvar_grid< cvm::real >::read_raw().

Referenced by colvarbias_meta::read_restart().

00118 {
00119   size_t const start_pos = is.tellg();
00120   std::string key, conf;
00121   if ((is >> key) && (key == std::string ("grid_parameters"))) {
00122     is.seekg (start_pos, std::ios::beg);
00123     is >> colvarparse::read_block ("grid_parameters", conf);
00124     parse_params (conf);
00125   } else {
00126     cvm::log ("Grid parameters are missing in the restart file, using those from the configuration.\n");
00127     is.seekg (start_pos, std::ios::beg);
00128   }
00129   read_raw (is);
00130   return is;
00131 }

virtual void colvar_grid_gradient::value_input (  std::vector< int > const &  ix,
cvm::real const &  new_value,
size_t const &  imult = 0,
bool  add = false
)  [inline, virtual]
 

Get the value from a formatted output and transform it into the internal representation (it may have been rescaled or manipulated).

Reimplemented from colvar_grid< cvm::real >.

Definition at line 1105 of file colvargrid.h.

References colvar_grid< cvm::real >::address(), colvar_grid_count::new_count(), samples, and colvar_grid< T >::value().

01109   {
01110     if (add) {
01111       if (samples)
01112         data[address (ix) + imult] += new_value * samples->new_count (ix);
01113       else
01114         data[address (ix) + imult] += new_value;
01115     } else {
01116       if (samples)
01117         data[address (ix) + imult] = new_value * samples->value (ix);
01118       else
01119         data[address (ix) + imult] = new_value;
01120     }
01121     has_data = true;
01122   }

virtual cvm::real colvar_grid_gradient::value_output (  std::vector< int > const &  ix,
size_t const &  imult = 0
)  [inline, virtual]
 

Return the value of the function at ix divided by its number of samples (if the count grid is defined).

Reimplemented from colvar_grid< cvm::real >.

Definition at line 1091 of file colvargrid.h.

References colvar_grid< cvm::real >::address(), colvarmodule::real, samples, and colvar_grid< T >::value().

01093   {
01094     if (samples)
01095       return (samples->value (ix) > 0) ?
01096         (data[address (ix) + imult] / cvm::real (samples->value (ix))) :
01097         0.0;
01098     else
01099       return data[address (ix) + imult];
01100   }

void colvar_grid_gradient::write_1D_integral (  std::ostream &  os  ) 
 

If the grid is 1-dimensional, integrate it and write the integral to a file.

Definition at line 140 of file colvargrid.C.

References average(), colvarmodule::fatal_error(), colvar_grid< cvm::real >::incr(), colvar_grid< cvm::real >::index_ok(), colvar_grid< cvm::real >::new_index(), colvarmodule::real, samples, colvar_grid< cvm::real >::value(), and colvar_grid< T >::value().

00141 {
00142   cvm::real bin, min, integral;
00143   std::vector<cvm::real> int_vals;
00144   
00145   os << "#       xi            A(xi)\n";
00146 
00147   if ( cv.size() != 1 ) {
00148     cvm::fatal_error ("Cannot write integral for multi-dimensional gradient grids.");
00149   }
00150 
00151   integral = 0.0;
00152   int_vals.push_back ( 0.0 );
00153   bin = 0.0;
00154   min = 0.0;
00155 
00156   // correction for periodic colvars, so that the PMF is periodic
00157   cvm::real corr;
00158   if ( periodic[0] ) {
00159     corr = average();
00160   } else {
00161     corr = 0.0;
00162   }
00163 
00164   for (std::vector<int> ix = new_index(); index_ok (ix); incr (ix), bin += 1.0 ) {
00165           
00166     if (samples) {
00167       size_t const samples_here = samples->value (ix);
00168       if (samples_here)
00169         integral += (value (ix) / cvm::real (samples_here) - corr) * cv[0]->width;
00170     } else {
00171       integral += (value (ix) - corr) * cv[0]->width;
00172     }
00173 
00174     if ( integral < min ) min = integral;
00175     int_vals.push_back ( integral );
00176   }
00177 
00178   bin = 0.0;
00179   for ( int i = 0; i < nx[0]; i++, bin += 1.0 ) {
00180     os << std::setw (10) << cv[0]->lower_boundary.real_value + cv[0]->width * bin << " "
00181        << std::setw (cvm::cv_width)
00182        << std::setprecision (cvm::cv_prec)
00183        << int_vals[i] - min << "\n";
00184   }
00185 
00186   os << std::setw (10) << cv[0]->lower_boundary.real_value + cv[0]->width * bin << " "
00187      << std::setw (cvm::cv_width)
00188      << std::setprecision (cvm::cv_prec)
00189      << int_vals[nx[0]] - min << "\n";
00190 
00191   return;
00192 }

std::ostream & colvar_grid_gradient::write_restart (  std::ostream &  os  ) 
 

Write the grid to a restart.

Definition at line 133 of file colvargrid.C.

References colvar_grid< cvm::real >::write_params(), and colvar_grid< cvm::real >::write_raw().

Referenced by colvarbias_meta::write_replica_state_file(), and colvarbias_meta::write_restart().

00134 {
00135   write_params (os);
00136   write_raw (os);
00137   return os;
00138 }

Member Data Documentation

colvar_grid_count* colvar_grid_gradient::samples
 

Provide the sample count by which each binned value should be divided.

Definition at line 1055 of file colvargrid.h.

Referenced by acc_force(), acc_grad(), average(), colvarbias_abf::colvarbias_abf(), value_input(), value_output(), and write_1D_integral().

The documentation for this class was generated from the following files:
Generated on Fri May 25 04:07:20 2012 for NAMD by  doxygen 1.3.9.1