forked from lijiext/lammps
1393 lines
41 KiB
C++
1393 lines
41 KiB
C++
/// -*- c++ -*-
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#ifndef COLVARGRID_H
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#define COLVARGRID_H
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#include <iostream>
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#include <iomanip>
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#include <cmath>
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#include "colvar.h"
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#include "colvarmodule.h"
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#include "colvarvalue.h"
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#include "colvarparse.h"
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/// \brief Grid of values of a function of several collective
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/// variables \param T The data type
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///
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/// Only scalar colvars supported so far: vector colvars are treated as arrays
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template <class T> class colvar_grid : public colvarparse {
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protected:
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/// Number of dimensions
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size_t nd;
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/// Number of points along each dimension
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std::vector<int> nx;
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/// Cumulative number of points along each dimension
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std::vector<int> nxc;
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/// \brief Multiplicity of each datum (allow the binning of
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/// non-scalar types such as atomic gradients)
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size_t mult;
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/// Total number of grid points
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size_t nt;
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/// Low-level array of values
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std::vector<T> data;
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/// Newly read data (used for count grids, when adding several grids read from disk)
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std::vector<size_t> new_data;
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/// Colvars collected in this grid
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std::vector<colvar *> cv;
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/// Do we request actual value (for extended-system colvars)?
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std::vector<bool> actual_value;
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/// Get the low-level index corresponding to an index
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inline size_t address(std::vector<int> const &ix) const
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{
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size_t addr = 0;
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for (size_t i = 0; i < nd; i++) {
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addr += ix[i]*nxc[i];
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if (cvm::debug()) {
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if (ix[i] >= nx[i]) {
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cvm::error("Error: exceeding bounds in colvar_grid.\n", BUG_ERROR);
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return 0;
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}
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}
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}
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return addr;
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}
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public:
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/// Lower boundaries of the colvars in this grid
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std::vector<colvarvalue> lower_boundaries;
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/// Upper boundaries of the colvars in this grid
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std::vector<colvarvalue> upper_boundaries;
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/// Whether some colvars are periodic
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std::vector<bool> periodic;
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/// Whether some colvars have hard lower boundaries
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std::vector<bool> hard_lower_boundaries;
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/// Whether some colvars have hard upper boundaries
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std::vector<bool> hard_upper_boundaries;
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/// Widths of the colvars in this grid
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std::vector<cvm::real> widths;
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/// True if this is a count grid related to another grid of data
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bool has_parent_data;
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/// Whether this grid has been filled with data or is still empty
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bool has_data;
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/// Return the number of colvars
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inline size_t number_of_colvars() const
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{
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return nd;
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}
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/// Return the number of points in the i-th direction, if provided, or
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/// the total number
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inline size_t number_of_points(int const icv = -1) const
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{
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if (icv < 0) {
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return nt;
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} else {
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return nx[icv];
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}
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}
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/// Get the sizes in each direction
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inline std::vector<int> const & sizes() const
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{
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return nx;
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}
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/// Set the sizes in each direction
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inline void set_sizes(std::vector<int> const &new_sizes)
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{
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nx = new_sizes;
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}
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/// Return the multiplicity of the type used
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inline size_t multiplicity() const
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{
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return mult;
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}
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/// \brief Allocate data
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int setup(std::vector<int> const &nx_i,
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T const &t = T(),
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size_t const &mult_i = 1)
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{
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if (cvm::debug()) {
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cvm::log("Allocating grid: multiplicity = "+cvm::to_str(mult_i)+
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", dimensions = "+cvm::to_str(nx_i)+".\n");
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}
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mult = mult_i;
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data.clear();
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nx = nx_i;
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nd = nx.size();
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nxc.resize(nd);
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// setup dimensions
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nt = mult;
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for (int i = nd-1; i >= 0; i--) {
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if (nx[i] <= 0) {
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cvm::error("Error: providing an invalid number of grid points, "+
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cvm::to_str(nx[i])+".\n", BUG_ERROR);
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return COLVARS_ERROR;
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}
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nxc[i] = nt;
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nt *= nx[i];
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}
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if (cvm::debug()) {
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cvm::log("Total number of grid elements = "+cvm::to_str(nt)+".\n");
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}
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data.reserve(nt);
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data.assign(nt, t);
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return COLVARS_OK;
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}
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/// \brief Allocate data (allow initialization also after construction)
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int setup()
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{
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return setup(this->nx, T(), this->mult);
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}
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/// \brief Reset data (in case the grid is being reused)
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void reset(T const &t = T())
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{
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data.assign(nt, t);
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}
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/// Default constructor
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colvar_grid() : has_data(false)
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{
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save_delimiters = false;
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nd = nt = 0;
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mult = 1;
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this->setup();
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}
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/// Destructor
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virtual ~colvar_grid()
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{}
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/// \brief "Almost copy-constructor": only copies configuration
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/// parameters from another grid, but doesn't reallocate stuff;
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/// setup() must be called after that;
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colvar_grid(colvar_grid<T> const &g) : nd(g.nd),
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nx(g.nx),
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mult(g.mult),
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data(),
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cv(g.cv),
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actual_value(g.actual_value),
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lower_boundaries(g.lower_boundaries),
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upper_boundaries(g.upper_boundaries),
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periodic(g.periodic),
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hard_lower_boundaries(g.hard_lower_boundaries),
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hard_upper_boundaries(g.hard_upper_boundaries),
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widths(g.widths),
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has_data(false)
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{
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save_delimiters = false;
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}
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/// \brief Constructor from explicit grid sizes \param nx_i Number
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/// of grid points along each dimension \param t Initial value for
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/// the function at each point (optional) \param mult_i Multiplicity
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/// of each value
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colvar_grid(std::vector<int> const &nx_i,
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T const &t = T(),
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size_t mult_i = 1)
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: has_data(false)
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{
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save_delimiters = false;
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this->setup(nx_i, t, mult_i);
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}
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/// \brief Constructor from a vector of colvars
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colvar_grid(std::vector<colvar *> const &colvars,
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T const &t = T(),
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size_t mult_i = 1,
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bool margin = false)
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: has_data(false)
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{
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save_delimiters = false;
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this->init_from_colvars(colvars, t, mult_i, margin);
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}
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int init_from_colvars(std::vector<colvar *> const &colvars,
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T const &t = T(),
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size_t mult_i = 1,
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bool margin = false)
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{
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if (cvm::debug()) {
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cvm::log("Reading grid configuration from collective variables.\n");
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}
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cv = colvars;
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nd = colvars.size();
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mult = mult_i;
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size_t i;
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for (i = 0; i < cv.size(); i++) {
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if (!cv[i]->tasks[colvar::task_lower_boundary] ||
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!cv[i]->tasks[colvar::task_upper_boundary]) {
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cvm::error("Tried to initialize a grid on a "
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"variable with undefined boundaries.\n", INPUT_ERROR);
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return COLVARS_ERROR;
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}
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}
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if (cvm::debug()) {
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cvm::log("Allocating a grid for "+cvm::to_str(colvars.size())+
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" collective variables, multiplicity = "+cvm::to_str(mult_i)+".\n");
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}
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for (i = 0; i < cv.size(); i++) {
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if (cv[i]->value().type() != colvarvalue::type_scalar) {
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cvm::error("Colvar grids can only be automatically "
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"constructed for scalar variables. "
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"ABF and histogram can not be used; metadynamics "
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"can be used with useGrids disabled.\n", INPUT_ERROR);
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return COLVARS_ERROR;
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}
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if (cv[i]->width <= 0.0) {
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cvm::error("Tried to initialize a grid on a "
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"variable with negative or zero width.\n", INPUT_ERROR);
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return COLVARS_ERROR;
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}
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widths.push_back(cv[i]->width);
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hard_lower_boundaries.push_back(cv[i]->hard_lower_boundary);
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hard_upper_boundaries.push_back(cv[i]->hard_upper_boundary);
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periodic.push_back(cv[i]->periodic_boundaries());
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// By default, get reported colvar value (for extended Lagrangian colvars)
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actual_value.push_back(false);
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// except if a colvar is specified twice in a row
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// then the first instance is the actual value
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if (i > 0 && cv[i-1] == cv[i]) {
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actual_value[i-1] = true;
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}
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if (margin) {
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if (periodic[i]) {
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// Shift the grid by half the bin width (values at edges instead of center of bins)
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lower_boundaries.push_back(cv[i]->lower_boundary.real_value - 0.5 * widths[i]);
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upper_boundaries.push_back(cv[i]->upper_boundary.real_value - 0.5 * widths[i]);
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} else {
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// Make this grid larger by one bin width
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lower_boundaries.push_back(cv[i]->lower_boundary.real_value - 0.5 * widths[i]);
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upper_boundaries.push_back(cv[i]->upper_boundary.real_value + 0.5 * widths[i]);
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}
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} else {
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lower_boundaries.push_back(cv[i]->lower_boundary);
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upper_boundaries.push_back(cv[i]->upper_boundary);
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}
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}
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this->init_from_boundaries();
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return this->setup();
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}
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int init_from_boundaries(T const &t = T(),
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size_t const &mult_i = 1)
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{
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if (cvm::debug()) {
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cvm::log("Configuring grid dimensions from colvars boundaries.\n");
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}
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// these will have to be updated
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nx.clear();
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nxc.clear();
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nt = 0;
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for (size_t i = 0; i < lower_boundaries.size(); i++) {
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cvm::real nbins = ( upper_boundaries[i].real_value -
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lower_boundaries[i].real_value ) / widths[i];
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int nbins_round = (int)(nbins+0.5);
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if (std::fabs(nbins - cvm::real(nbins_round)) > 1.0E-10) {
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cvm::log("Warning: grid interval("+
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cvm::to_str(lower_boundaries[i], cvm::cv_width, cvm::cv_prec)+" - "+
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cvm::to_str(upper_boundaries[i], cvm::cv_width, cvm::cv_prec)+
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") is not commensurate to its bin width("+
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cvm::to_str(widths[i], cvm::cv_width, cvm::cv_prec)+").\n");
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upper_boundaries[i].real_value = lower_boundaries[i].real_value +
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(nbins_round * widths[i]);
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}
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if (cvm::debug())
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cvm::log("Number of points is "+cvm::to_str((int) nbins_round)+
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" for the colvar no. "+cvm::to_str(i+1)+".\n");
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nx.push_back(nbins_round);
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}
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return COLVARS_OK;
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}
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/// Wrap an index vector around periodic boundary conditions
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/// also checks validity of non-periodic indices
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inline void wrap(std::vector<int> & ix) const
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{
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for (size_t i = 0; i < nd; i++) {
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if (periodic[i]) {
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ix[i] = (ix[i] + nx[i]) % nx[i]; //to ensure non-negative result
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} else {
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if (ix[i] < 0 || ix[i] >= nx[i]) {
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cvm::error("Trying to wrap illegal index vector (non-PBC) for a grid point: "
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+ cvm::to_str(ix), BUG_ERROR);
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return;
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}
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}
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}
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}
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/// \brief Report the bin corresponding to the current value of variable i
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inline int current_bin_scalar(int const i) const
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{
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return value_to_bin_scalar(actual_value[i] ? cv[i]->actual_value() : cv[i]->value(), i);
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}
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/// \brief Use the lower boundary and the width to report which bin
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/// the provided value is in
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inline int value_to_bin_scalar(colvarvalue const &value, const int i) const
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{
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return (int) std::floor( (value.real_value - lower_boundaries[i].real_value) / widths[i] );
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}
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/// \brief Same as the standard version, but uses another grid definition
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inline int value_to_bin_scalar(colvarvalue const &value,
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colvarvalue const &new_offset,
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cvm::real const &new_width) const
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{
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return (int) std::floor( (value.real_value - new_offset.real_value) / new_width );
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}
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/// \brief Use the two boundaries and the width to report the
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/// central value corresponding to a bin index
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inline colvarvalue bin_to_value_scalar(int const &i_bin, int const i) const
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{
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return lower_boundaries[i].real_value + widths[i] * (0.5 + i_bin);
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}
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/// \brief Same as the standard version, but uses different parameters
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inline colvarvalue bin_to_value_scalar(int const &i_bin,
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colvarvalue const &new_offset,
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cvm::real const &new_width) const
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{
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return new_offset.real_value + new_width * (0.5 + i_bin);
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}
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/// Set the value at the point with index ix
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inline void set_value(std::vector<int> const &ix,
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T const &t,
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size_t const &imult = 0)
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{
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data[this->address(ix)+imult] = t;
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has_data = true;
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}
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/// \brief Get the change from this to other_grid
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/// and store the result in this.
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/// this_grid := other_grid - this_grid
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/// Grids must have the same dimensions.
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void delta_grid(colvar_grid<T> const &other_grid)
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{
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if (other_grid.multiplicity() != this->multiplicity()) {
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cvm::error("Error: trying to subtract two grids with "
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"different multiplicity.\n");
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return;
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}
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if (other_grid.data.size() != this->data.size()) {
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cvm::error("Error: trying to subtract two grids with "
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"different size.\n");
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return;
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}
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for (size_t i = 0; i < data.size(); i++) {
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data[i] = other_grid.data[i] - data[i];
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}
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has_data = true;
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}
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/// \brief Copy data from another grid of the same type, AND
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/// identical definition (boundaries, widths)
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/// Added for shared ABF.
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void copy_grid(colvar_grid<T> const &other_grid)
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{
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if (other_grid.multiplicity() != this->multiplicity()) {
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cvm::error("Error: trying to copy two grids with "
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"different multiplicity.\n");
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return;
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}
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if (other_grid.data.size() != this->data.size()) {
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cvm::error("Error: trying to copy two grids with "
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"different size.\n");
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return;
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}
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for (size_t i = 0; i < data.size(); i++) {
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data[i] = other_grid.data[i];
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}
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has_data = true;
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}
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/// \brief Extract the grid data as they are represented in memory.
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/// Put the results in "out_data".
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void raw_data_out(T* out_data) const
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{
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for (size_t i = 0; i < data.size(); i++) out_data[i] = data[i];
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}
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/// \brief Input the data as they are represented in memory.
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void raw_data_in(const T* in_data)
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{
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for (size_t i = 0; i < data.size(); i++) data[i] = in_data[i];
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has_data = true;
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}
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/// \brief Size of the data as they are represented in memory.
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size_t raw_data_num() const { return data.size(); }
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/// \brief Get the binned value indexed by ix, or the first of them
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/// if the multiplicity is larger than 1
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inline T const & value(std::vector<int> const &ix,
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size_t const &imult = 0) const
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{
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return data[this->address(ix) + imult];
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}
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/// \brief Add a constant to all elements (fast loop)
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inline void add_constant(T const &t)
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{
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for (size_t i = 0; i < nt; i++)
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data[i] += t;
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has_data = true;
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}
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/// \brief Multiply all elements by a scalar constant (fast loop)
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inline void multiply_constant(cvm::real const &a)
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{
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for (size_t i = 0; i < nt; i++)
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data[i] *= a;
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}
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/// \brief Get the bin indices corresponding to the provided values of
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/// the colvars
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inline std::vector<int> const get_colvars_index(std::vector<colvarvalue> const &values) const
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{
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std::vector<int> index = new_index();
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for (size_t i = 0; i < nd; i++) {
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index[i] = value_to_bin_scalar(values[i], i);
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}
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return index;
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}
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/// \brief Get the bin indices corresponding to the current values
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/// of the colvars
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inline std::vector<int> const get_colvars_index() const
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{
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std::vector<int> index = new_index();
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for (size_t i = 0; i < nd; i++) {
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index[i] = current_bin_scalar(i);
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}
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return index;
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}
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|
|
|
/// \brief Get the minimal distance (in number of bins) from the
|
|
/// boundaries; a negative number is returned if the given point is
|
|
/// off-grid
|
|
inline cvm::real bin_distance_from_boundaries(std::vector<colvarvalue> const &values,
|
|
bool skip_hard_boundaries = false)
|
|
{
|
|
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 ( ((!skip_hard_boundaries) || (!hard_lower_boundaries[i])) && (dl < minimum))
|
|
minimum = dl;
|
|
if ( ((!skip_hard_boundaries) || (!hard_upper_boundaries[i])) && (du < minimum))
|
|
minimum = du;
|
|
}
|
|
|
|
return minimum;
|
|
}
|
|
|
|
|
|
/// \brief 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.
|
|
void map_grid(colvar_grid<T> const &other_grid)
|
|
{
|
|
if (other_grid.multiplicity() != this->multiplicity()) {
|
|
cvm::error("Error: trying to merge two grids with values of "
|
|
"different multiplicity.\n");
|
|
return;
|
|
}
|
|
|
|
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");
|
|
}
|
|
|
|
/// \brief Add data from another grid of the same type, AND
|
|
/// identical definition (boundaries, widths)
|
|
void add_grid(colvar_grid<T> const &other_grid,
|
|
cvm::real scale_factor = 1.0)
|
|
{
|
|
if (other_grid.multiplicity() != this->multiplicity()) {
|
|
cvm::error("Error: trying to sum togetehr two grids with values of "
|
|
"different multiplicity.\n");
|
|
return;
|
|
}
|
|
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;
|
|
}
|
|
|
|
/// \brief Return the value suitable for output purposes (so that it
|
|
/// may be rescaled or manipulated without changing it permanently)
|
|
virtual inline T value_output(std::vector<int> const &ix,
|
|
size_t const &imult = 0)
|
|
{
|
|
return value(ix, imult);
|
|
}
|
|
|
|
/// \brief 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)
|
|
virtual inline void value_input(std::vector<int> const &ix,
|
|
T const &t,
|
|
size_t const &imult = 0,
|
|
bool add = false)
|
|
{
|
|
if ( add )
|
|
data[address(ix) + imult] += t;
|
|
else
|
|
data[address(ix) + imult] = t;
|
|
has_data = true;
|
|
}
|
|
|
|
// /// Get the pointer to the binned value indexed by ix
|
|
// inline T const *value_p (std::vector<int> const &ix)
|
|
// {
|
|
// return &(data[address (ix)]);
|
|
// }
|
|
|
|
/// \brief Get the index corresponding to the "first" bin, to be
|
|
/// used as the initial value for an index in looping
|
|
inline std::vector<int> const new_index() const
|
|
{
|
|
return std::vector<int> (nd, 0);
|
|
}
|
|
|
|
/// \brief Check that the index is within range in each of the
|
|
/// dimensions
|
|
inline bool index_ok(std::vector<int> const &ix) const
|
|
{
|
|
for (size_t i = 0; i < nd; i++) {
|
|
if ( (ix[i] < 0) || (ix[i] >= int(nx[i])) )
|
|
return false;
|
|
}
|
|
return true;
|
|
}
|
|
|
|
/// \brief Increment the index, in a way that will make it loop over
|
|
/// the whole nd-dimensional array
|
|
inline void incr(std::vector<int> &ix) const
|
|
{
|
|
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;
|
|
}
|
|
}
|
|
}
|
|
|
|
/// \brief Write the grid parameters (number of colvars, boundaries, width and number of points)
|
|
std::ostream & write_params(std::ostream &os)
|
|
{
|
|
size_t i;
|
|
os << "grid_parameters {\n n_colvars " << nd << "\n";
|
|
|
|
os << " lower_boundaries ";
|
|
for (i = 0; i < nd; i++)
|
|
os << " " << lower_boundaries[i];
|
|
os << "\n";
|
|
|
|
os << " upper_boundaries ";
|
|
for (i = 0; i < nd; i++)
|
|
os << " " << upper_boundaries[i];
|
|
os << "\n";
|
|
|
|
os << " widths ";
|
|
for (i = 0; i < nd; i++)
|
|
os << " " << widths[i];
|
|
os << "\n";
|
|
|
|
os << " sizes ";
|
|
for (i = 0; i < nd; i++)
|
|
os << " " << nx[i];
|
|
os << "\n";
|
|
|
|
os << "}\n";
|
|
return os;
|
|
}
|
|
|
|
/// Read a grid definition from a config string
|
|
int parse_params(std::string const &conf)
|
|
{
|
|
if (cvm::debug()) cvm::log("Reading grid configuration from string.\n");
|
|
|
|
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::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");
|
|
return COLVARS_ERROR;
|
|
}
|
|
}
|
|
|
|
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);
|
|
|
|
// support also camel case
|
|
colvarparse::get_keyval(conf, "lowerBoundaries",
|
|
lower_boundaries, lower_boundaries, colvarparse::parse_silent);
|
|
colvarparse::get_keyval(conf, "upperBoundaries",
|
|
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);
|
|
|
|
if (nd < lower_boundaries.size()) nd = lower_boundaries.size();
|
|
|
|
if (! actual_value.size()) actual_value.assign(nd, false);
|
|
if (! periodic.size()) periodic.assign(nd, false);
|
|
if (! widths.size()) widths.assign(nd, 1.0);
|
|
|
|
bool new_params = false;
|
|
if (old_nx.size()) {
|
|
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;
|
|
}
|
|
}
|
|
} else {
|
|
new_params = true;
|
|
}
|
|
|
|
// reallocate the array in case the grid params have just changed
|
|
if (new_params) {
|
|
init_from_boundaries();
|
|
// data.resize(0); // no longer needed: setup calls clear()
|
|
return this->setup(nx, T(), mult);
|
|
}
|
|
|
|
return COLVARS_OK;
|
|
}
|
|
|
|
/// \brief Check that the grid information inside (boundaries,
|
|
/// widths, ...) is consistent with the current setting of the
|
|
/// colvars
|
|
void check_consistency()
|
|
{
|
|
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::error("Error: restart information for a grid is "
|
|
"inconsistent with that of its colvars.\n");
|
|
return;
|
|
}
|
|
}
|
|
}
|
|
|
|
|
|
/// \brief Check that the grid information inside (boundaries,
|
|
/// widths, ...) is consistent with that of another grid
|
|
void check_consistency(colvar_grid<T> const &other_grid)
|
|
{
|
|
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::error("Error: inconsistency between "
|
|
"two grids that are supposed to be equal, "
|
|
"aside from the data stored.\n");
|
|
return;
|
|
}
|
|
}
|
|
}
|
|
|
|
|
|
/// \brief Read grid entry in restart file
|
|
std::istream & read_restart(std::istream &is)
|
|
{
|
|
size_t const start_pos = is.tellg();
|
|
std::string key, conf;
|
|
if ((is >> key) && (key == std::string("grid_parameters"))) {
|
|
is.seekg(start_pos, std::ios::beg);
|
|
is >> colvarparse::read_block("grid_parameters", conf);
|
|
parse_params(conf);
|
|
} else {
|
|
cvm::log("Grid parameters are missing in the restart file, using those from the configuration.\n");
|
|
is.seekg(start_pos, std::ios::beg);
|
|
}
|
|
read_raw(is);
|
|
return is;
|
|
}
|
|
|
|
/// \brief Write grid entry in restart file
|
|
std::ostream & write_restart(std::ostream &os)
|
|
{
|
|
write_params(os);
|
|
write_raw(os);
|
|
return os;
|
|
}
|
|
|
|
|
|
/// \brief Write the grid data without labels, as they are
|
|
/// represented in memory
|
|
/// \param buf_size Number of values per line
|
|
std::ostream & write_raw(std::ostream &os,
|
|
size_t const buf_size = 3)
|
|
{
|
|
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;
|
|
}
|
|
|
|
/// \brief Read data written by colvar_grid::write_raw()
|
|
std::istream & read_raw(std::istream &is)
|
|
{
|
|
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);
|
|
cvm::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");
|
|
return is;
|
|
}
|
|
}
|
|
}
|
|
|
|
has_data = true;
|
|
return is;
|
|
}
|
|
|
|
/// \brief Write the grid in a format which is both human readable
|
|
/// and suitable for visualization e.g. with gnuplot
|
|
void write_multicol(std::ostream &os)
|
|
{
|
|
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";
|
|
}
|
|
}
|
|
|
|
/// \brief Read a grid written by colvar_grid::write_multicol()
|
|
/// Adding data if add is true, replacing if false
|
|
std::istream & read_multicol(std::istream &is, bool add = false)
|
|
{
|
|
// 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::error("Cannot read grid file: missing reference to colvars.");
|
|
return is;
|
|
}
|
|
|
|
if ( !(is >> hash) || (hash != "#") ) {
|
|
cvm::error("Error reading grid at position "+
|
|
cvm::to_str(is.tellg())+" in stream(read \"" + hash + "\")\n");
|
|
return is;
|
|
}
|
|
|
|
is >> n;
|
|
if ( n != nd ) {
|
|
cvm::error("Error reading grid: wrong number of collective variables.\n");
|
|
return is;
|
|
}
|
|
|
|
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::error("Error reading grid at position "+
|
|
cvm::to_str(is.tellg())+" in stream(read \"" + hash + "\")\n");
|
|
return is;
|
|
}
|
|
|
|
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;
|
|
}
|
|
|
|
/// \brief Write the grid data without labels, as they are
|
|
/// represented in memory
|
|
/// \param buf_size Number of values per line
|
|
std::ostream & write_opendx(std::ostream &os)
|
|
{
|
|
// write the header
|
|
os << "object 1 class gridpositions counts";
|
|
int icv;
|
|
for (icv = 0; icv < number_of_colvars(); icv++) {
|
|
os << " " << number_of_points(icv);
|
|
}
|
|
os << "\n";
|
|
|
|
os << "origin";
|
|
for (icv = 0; icv < number_of_colvars(); icv++) {
|
|
os << " " << (lower_boundaries[icv].real_value + 0.5 * widths[icv]);
|
|
}
|
|
os << "\n";
|
|
|
|
for (icv = 0; icv < number_of_colvars(); icv++) {
|
|
os << "delta";
|
|
for (size_t icv2 = 0; icv2 < number_of_colvars(); icv2++) {
|
|
if (icv == icv2) os << " " << widths[icv];
|
|
else os << " " << 0.0;
|
|
}
|
|
os << "\n";
|
|
}
|
|
|
|
os << "object 2 class gridconnections counts";
|
|
for (icv = 0; icv < number_of_colvars(); icv++) {
|
|
os << " " << number_of_points(icv);
|
|
}
|
|
os << "\n";
|
|
|
|
os << "object 3 class array type double rank 0 items "
|
|
<< number_of_points() << " data follows\n";
|
|
|
|
write_raw(os);
|
|
|
|
os << "object \"collective variables scalar field\" class field\n";
|
|
return os;
|
|
}
|
|
};
|
|
|
|
|
|
|
|
/// \brief Colvar_grid derived class to hold counters in discrete
|
|
/// n-dim colvar space
|
|
class colvar_grid_count : public colvar_grid<size_t>
|
|
{
|
|
public:
|
|
|
|
/// Default constructor
|
|
colvar_grid_count();
|
|
|
|
/// Destructor
|
|
virtual inline ~colvar_grid_count()
|
|
{}
|
|
|
|
/// Constructor
|
|
colvar_grid_count(std::vector<int> const &nx_i,
|
|
size_t const &def_count = 0);
|
|
|
|
/// Constructor from a vector of colvars
|
|
colvar_grid_count(std::vector<colvar *> &colvars,
|
|
size_t const &def_count = 0);
|
|
|
|
/// Increment the counter at given position
|
|
inline void incr_count(std::vector<int> const &ix)
|
|
{
|
|
++(data[this->address(ix)]);
|
|
}
|
|
|
|
/// \brief Get the binned count indexed by ix from the newly read data
|
|
inline size_t const & new_count(std::vector<int> const &ix,
|
|
size_t const &imult = 0)
|
|
{
|
|
return new_data[address(ix) + imult];
|
|
}
|
|
|
|
/// \brief Get the value from a formatted output and transform it
|
|
/// into the internal representation (it may have been rescaled or
|
|
/// manipulated)
|
|
virtual inline void value_input(std::vector<int> const &ix,
|
|
size_t const &t,
|
|
size_t const &imult = 0,
|
|
bool add = false)
|
|
{
|
|
if (add) {
|
|
data[address(ix)] += t;
|
|
if (this->has_parent_data) {
|
|
// save newly read data for inputting parent grid
|
|
new_data[address(ix)] = t;
|
|
}
|
|
} else {
|
|
data[address(ix)] = t;
|
|
}
|
|
has_data = true;
|
|
}
|
|
};
|
|
|
|
|
|
/// Class for accumulating a scalar function on a grid
|
|
class colvar_grid_scalar : public colvar_grid<cvm::real>
|
|
{
|
|
public:
|
|
|
|
/// \brief Provide the associated sample count by which each binned value
|
|
/// should be divided
|
|
colvar_grid_count *samples;
|
|
|
|
/// Default constructor
|
|
colvar_grid_scalar();
|
|
|
|
/// Copy constructor (needed because of the grad pointer)
|
|
colvar_grid_scalar(colvar_grid_scalar const &g);
|
|
|
|
/// Destructor
|
|
~colvar_grid_scalar();
|
|
|
|
/// Constructor from specific sizes arrays
|
|
colvar_grid_scalar(std::vector<int> const &nx_i);
|
|
|
|
/// Constructor from a vector of colvars
|
|
colvar_grid_scalar(std::vector<colvar *> &colvars,
|
|
bool margin = 0);
|
|
|
|
/// Accumulate the value
|
|
inline void acc_value(std::vector<int> const &ix,
|
|
cvm::real const &new_value,
|
|
size_t const &imult = 0)
|
|
{
|
|
// only legal value of imult here is 0
|
|
data[address(ix)] += new_value;
|
|
if (samples)
|
|
samples->incr_count(ix);
|
|
has_data = true;
|
|
}
|
|
|
|
/// Return the gradient of the scalar field from finite differences
|
|
inline const cvm::real * gradient_finite_diff( const std::vector<int> &ix0 )
|
|
{
|
|
cvm::real A0, A1;
|
|
std::vector<int> ix;
|
|
if (nd != 2) {
|
|
cvm::error("Finite differences available in dimension 2 only.");
|
|
return grad;
|
|
}
|
|
for (unsigned int n = 0; n < nd; n++) {
|
|
ix = ix0;
|
|
A0 = data[address(ix)];
|
|
ix[n]++; wrap(ix);
|
|
A1 = data[address(ix)];
|
|
ix[1-n]++; wrap(ix);
|
|
A1 += data[address(ix)];
|
|
ix[n]--; wrap(ix);
|
|
A0 += data[address(ix)];
|
|
grad[n] = 0.5 * (A1 - A0) / widths[n];
|
|
}
|
|
return grad;
|
|
}
|
|
|
|
/// \brief Return the value of the function at ix divided by its
|
|
/// number of samples (if the count grid is defined)
|
|
virtual cvm::real value_output(std::vector<int> const &ix,
|
|
size_t const &imult = 0)
|
|
{
|
|
if (imult > 0) {
|
|
cvm::error("Error: trying to access a component "
|
|
"larger than 1 in a scalar data grid.\n");
|
|
return 0.;
|
|
}
|
|
if (samples) {
|
|
return (samples->value(ix) > 0) ?
|
|
(data[address(ix)] / cvm::real(samples->value(ix))) :
|
|
0.0;
|
|
} else {
|
|
return data[address(ix)];
|
|
}
|
|
}
|
|
|
|
/// \brief Get the value from a formatted output and transform it
|
|
/// into the internal representation (it may have been rescaled or
|
|
/// manipulated)
|
|
virtual void value_input(std::vector<int> const &ix,
|
|
cvm::real const &new_value,
|
|
size_t const &imult = 0,
|
|
bool add = false)
|
|
{
|
|
if (imult > 0) {
|
|
cvm::error("Error: trying to access a component "
|
|
"larger than 1 in a scalar data grid.\n");
|
|
return;
|
|
}
|
|
if (add) {
|
|
if (samples)
|
|
data[address(ix)] += new_value * samples->new_count(ix);
|
|
else
|
|
data[address(ix)] += new_value;
|
|
} else {
|
|
if (samples)
|
|
data[address(ix)] = new_value * samples->value(ix);
|
|
else
|
|
data[address(ix)] = new_value;
|
|
}
|
|
has_data = true;
|
|
}
|
|
|
|
/// \brief Return the highest value
|
|
cvm::real maximum_value() const;
|
|
|
|
/// \brief Return the lowest value
|
|
cvm::real minimum_value() const;
|
|
|
|
/// \brief Calculates the integral of the map (uses widths if they are defined)
|
|
cvm::real integral() const;
|
|
|
|
/// \brief Assuming that the map is a normalized probability density,
|
|
/// calculates the entropy (uses widths if they are defined)
|
|
cvm::real entropy() const;
|
|
|
|
private:
|
|
// gradient
|
|
cvm::real * grad;
|
|
};
|
|
|
|
|
|
|
|
/// Class for accumulating the gradient of a scalar function on a grid
|
|
class colvar_grid_gradient : public colvar_grid<cvm::real>
|
|
{
|
|
public:
|
|
|
|
/// \brief Provide the sample count by which each binned value
|
|
/// should be divided
|
|
colvar_grid_count *samples;
|
|
|
|
/// Default constructor
|
|
colvar_grid_gradient();
|
|
|
|
/// Destructor
|
|
virtual inline ~colvar_grid_gradient()
|
|
{}
|
|
|
|
/// Constructor from specific sizes arrays
|
|
colvar_grid_gradient(std::vector<int> const &nx_i);
|
|
|
|
/// Constructor from a vector of colvars
|
|
colvar_grid_gradient(std::vector<colvar *> &colvars);
|
|
|
|
/// \brief Accumulate the gradient
|
|
inline void acc_grad(std::vector<int> const &ix, cvm::real const *grads) {
|
|
for (size_t imult = 0; imult < mult; imult++) {
|
|
data[address(ix) + imult] += grads[imult];
|
|
}
|
|
if (samples)
|
|
samples->incr_count(ix);
|
|
}
|
|
|
|
/// \brief Accumulate the gradient based on the force (i.e. sums the
|
|
/// opposite of the force)
|
|
inline void acc_force(std::vector<int> const &ix, cvm::real const *forces) {
|
|
for (size_t imult = 0; imult < mult; imult++) {
|
|
data[address(ix) + imult] -= forces[imult];
|
|
}
|
|
if (samples)
|
|
samples->incr_count(ix);
|
|
}
|
|
|
|
/// \brief Return the value of the function at ix divided by its
|
|
/// number of samples (if the count grid is defined)
|
|
virtual inline cvm::real value_output(std::vector<int> const &ix,
|
|
size_t const &imult = 0)
|
|
{
|
|
if (samples)
|
|
return (samples->value(ix) > 0) ?
|
|
(data[address(ix) + imult] / cvm::real(samples->value(ix))) :
|
|
0.0;
|
|
else
|
|
return data[address(ix) + imult];
|
|
}
|
|
|
|
/// \brief Get the value from a formatted output and transform it
|
|
/// into the internal representation (it may have been rescaled or
|
|
/// manipulated)
|
|
virtual inline void value_input(std::vector<int> const &ix,
|
|
cvm::real const &new_value,
|
|
size_t const &imult = 0,
|
|
bool add = false)
|
|
{
|
|
if (add) {
|
|
if (samples)
|
|
data[address(ix) + imult] += new_value * samples->new_count(ix);
|
|
else
|
|
data[address(ix) + imult] += new_value;
|
|
} else {
|
|
if (samples)
|
|
data[address(ix) + imult] = new_value * samples->value(ix);
|
|
else
|
|
data[address(ix) + imult] = new_value;
|
|
}
|
|
has_data = true;
|
|
}
|
|
|
|
|
|
/// Compute and return average value for a 1D gradient grid
|
|
inline cvm::real average()
|
|
{
|
|
size_t n = 0;
|
|
|
|
if (nd != 1 || nx[0] == 0) {
|
|
return 0.0;
|
|
}
|
|
|
|
cvm::real sum = 0.0;
|
|
std::vector<int> ix = new_index();
|
|
if (samples) {
|
|
for ( ; index_ok(ix); incr(ix)) {
|
|
if ( (n = samples->value(ix)) )
|
|
sum += value(ix) / n;
|
|
}
|
|
} else {
|
|
for ( ; index_ok(ix); incr(ix)) {
|
|
sum += value(ix);
|
|
}
|
|
}
|
|
return (sum / cvm::real(nx[0]));
|
|
}
|
|
|
|
/// \brief If the grid is 1-dimensional, integrate it and write the
|
|
/// integral to a file
|
|
void write_1D_integral(std::ostream &os);
|
|
|
|
};
|
|
|
|
|
|
#endif
|
|
|