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lammps/tools/colvars/abf_data.h
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abf_data.h
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/// \file integrate.h General headers for ABF_integrate
#include <iostream>
#include <vector>
#define MIN_SAMPLES 1
/// Free energy gradients class
class ABFdata {
protected:
/// Sizes of (i-1) dimension blocks
/// computed as Prod_(j<i) sizes[j]
int *blocksizes;
/// Minimum values of each variable
double *mins;
public:
int Nvars;
/// Free energy gradients (vector field)
double *gradients;
/// Sampling from the ABF calculation
unsigned int *count;
/// Bin widths
double *widths;
unsigned int scalar_dim;
unsigned int vec_dim;
unsigned int *histogram;
/// History-dependent bias
double *bias;
/// Estimate of the FE gradient computed
/// from MtD bias or histogram in standard MC
double *estimate;
/// Deviation between starting free energy gradient and
/// estimated one
double *deviation;
void write_histogram(const char *fileName);
void write_bias(const char *fileName);
void write_field(double *field, const char *fileName);
/// Grid sizes
int *sizes;
/// Flag stating if each variable is periodic
int *PBC;
/// Constructor: reads from a file
ABFdata(const char *gradFileName);
~ABFdata();
/// \brief Returns an offset for scalar fields based on a n-index.
/// multiply by Nvars to get an offset in a Nvars-vector field
unsigned int offset(const int *);
inline bool wrap(int &pos, int i);
/// Decides if an offset is outside the allowed region based on the ABF sampling
inline bool allowed(unsigned int offset);
};
inline bool ABFdata::wrap(int &pos, int i)
{
if (PBC[i]) {
if (pos == -1) {
pos = sizes[i] - 1;
return true;
}
if (pos == sizes[i]) {
pos = 0;
return true;
}
} else {
// No PBC
if (pos == -1) {
pos = 0;
return false;
}
if (pos == sizes[i]) {
pos = sizes[i] - 1;
return false;
}
}
return true;
}
inline bool ABFdata::allowed(unsigned int offset) {
return count[offset] > MIN_SAMPLES;
}
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