colvarcomp_coordnums.h

// -*- c++ -*-
 
// This file is part of the Collective Variables module (Colvars).
// The original version of Colvars and its updates are located at:
// https://github.com/Colvars/colvars
// Please update all Colvars source files before making any changes.
// If you wish to distribute your changes, please submit them to the
// Colvars repository at GitHub.
//
 
#ifndef COLVARCOMP_COORDNUM_H
#define COLVARCOMP_COORDNUM_H
 
#include <memory>
 
#include "colvar.h"
#include "colvarcomp.h"
#include "colvarmodule.h"
 
 
class colvar::coordnum : public colvar::cvc {
public:
 
  coordnum();
  virtual ~coordnum();
  virtual int init(std::string const &conf);
  virtual void calc_value();
  virtual void calc_gradients();
 
  enum {
    ef_null = 0,
    ef_gradients = 1,
    ef_use_internal_pbc = (1 << 8),
    ef_use_pairlist = (1 << 9),
    ef_rebuild_pairlist = (1 << 10)
  };
 
  template <int flags>
  static cvm::real switching_function(cvm::real const &l2, cvm::real &dFdl2, int en, int ed,
                                      cvm::real pairlist_tol);
 
  template <int flags>
  static cvm::real compute_pair_coordnum(cvm::rvector const &inv_r0_vec,
                                         cvm::rvector const &inv_r0sq_vec, int en, int ed,
                                         const cvm::real a1x, const cvm::real a1y, const cvm::real a1z,
                                         const cvm::real a2x, const cvm::real a2y, const cvm::real a2z,
                                         cvm::real &g1x, cvm::real &g1y, cvm::real &g1z,
                                         cvm::real &g2x, cvm::real &g2y, cvm::real &g2z,
                                         cvm::real pairlist_tol, cvm::real pairlist_tol_l2_max,
                                         colvarmodule *cvmodule);
 
  template <bool use_group1_com, bool use_group2_com, int flags> int compute_coordnum();
 
  template <bool use_group1_com, bool use_group2_com, int flags> void main_loop();
 
protected:
  cvm::atom_group *group1 = nullptr;
  cvm::atom_group *group2 = nullptr;
 
  cvm::rvector r0_vec;
 
  cvm::rvector inv_r0_vec;
 
  cvm::rvector inv_r0sq_vec;
 
  void update_cutoffs(cvm::rvector const &r0_vec_i);
 
  int en = 6;
  int ed = 12;
 
  size_t num_pairs = 0;
 
  bool b_group1_center_only = false;
 
  bool b_group2_center_only = false;
 
  bool b_use_internal_pbc = false;
 
  cvm::real tolerance = 0.0;
 
  cvm::real tolerance_l2_max = 1.0e20;
 
  void compute_tolerance_l2_max();
 
  int pairlist_freq = 100;
 
  std::unique_ptr<bool []> pairlist;
 
};
 
 
class colvar::selfcoordnum : public colvar::coordnum {
public:
 
  selfcoordnum();
  virtual void calc_value();
  virtual void calc_gradients();
 
  template <int flags> void selfcoordnum_sequential_loop();
 
  template <int flags> int compute_selfcoordnum();
};
 
 
class colvar::groupcoordnum : public colvar::coordnum {
public:
  groupcoordnum();
  virtual ~groupcoordnum() {}
  virtual void calc_value();
  virtual void calc_gradients();
};
 
 
class colvar::h_bond : public colvar::cvc {
public:
  h_bond(cvm::atom_group::simple_atom const &acceptor, cvm::atom_group::simple_atom const &donor,
         cvm::real r0, int en, int ed);
  h_bond();
  virtual ~h_bond() {}
  virtual int init(std::string const &conf);
  virtual void calc_value();
  virtual void calc_gradients();
 
protected:
  cvm::rvector r0_vec;
  int en = 6;
  int ed = 8;
};
 
 
template <int flags>
inline cvm::real colvar::coordnum::switching_function(cvm::real const &l2, cvm::real &dFdl2,
                                               int en, int ed,
                                               cvm::real pairlist_tol)
{
  // Assume en and ed are even integers, and avoid sqrt in the following
  int const en2 = en/2;
  int const ed2 = ed/2;
 
  cvm::real const xn = cvm::integer_power(l2, en2);
  cvm::real const xd = cvm::integer_power(l2, ed2);
  cvm::real const eps_l2 = 1.0e-7;
  cvm::real const h = l2 - 1.0;
  cvm::real const en2_r = (cvm::real) en2;
  cvm::real const ed2_r = (cvm::real) ed2;
  cvm::real func_no_pairlist;
 
  if (std::abs(h) < eps_l2) {
    // Order-2 Taylor expansion: c0 + c1*h + c2*h^2
    cvm::real const c0 = en2_r / ed2_r;
    cvm::real const c1 = (en2_r * (en2_r - ed2_r)) / (2.0 * ed2_r);
    cvm::real const c2 = (en2_r * (en2_r - ed2_r) * (2.0 * en2_r - ed2_r - 3.0)) / (12.0 * ed2_r);
    func_no_pairlist = c0 + h * (c1 + h * c2);
  } else {
    func_no_pairlist = (1.0 - xn) / (1.0 - xd);
  }
 
  cvm::real func, inv_one_pairlist_tol;
  if (flags & ef_use_pairlist) {
    inv_one_pairlist_tol = 1 / (1.0-pairlist_tol);
    func = (func_no_pairlist - pairlist_tol) * inv_one_pairlist_tol;
  } else {
    func = func_no_pairlist;
  }
 
  // If the value is too small and we are correcting for the tolerance, the result is negative
  // and we need to exclude it rather than let it contribute to the sum or the gradients.
  if (func < 0)
    return 0;
 
  if (flags & ef_gradients) {
    // Logarithmic derivative: 1st-order Taylor expansion around l2 = 1
    cvm::real log_deriv;
    if (std::abs(h) < eps_l2) {
      cvm::real const g0 = 0.5 * (en2_r - ed2_r);
      cvm::real const g1 = ((en2_r - ed2_r) * (en2_r + ed2_r - 6.0)) / 12.0;
      log_deriv = g0 + h * g1;
    } else {
      log_deriv = (ed2_r * xd / ((1.0 - xd) * l2)) - (en2_r * xn / ((1.0 - xn) * l2));
    }
    dFdl2 = (flags & ef_use_pairlist) ?
      func_no_pairlist * inv_one_pairlist_tol * log_deriv :
      func * log_deriv;
  }
 
  return func;
}
 
 
template<int flags>
inline cvm::real colvar::coordnum::compute_pair_coordnum(cvm::rvector const &inv_r0_vec,
                                                         cvm::rvector const &inv_r0sq_vec,
                                                         int en,
                                                         int ed,
                                                         const cvm::real a1x,
                                                         const cvm::real a1y,
                                                         const cvm::real a1z,
                                                         const cvm::real a2x,
                                                         const cvm::real a2y,
                                                         const cvm::real a2z,
                                                         cvm::real& g1x,
                                                         cvm::real& g1y,
                                                         cvm::real& g1z,
                                                         cvm::real& g2x,
                                                         cvm::real& g2y,
                                                         cvm::real& g2z,
                                                         cvm::real pairlist_tol,
                                                         cvm::real pairlist_tol_l2_max,
                                                         colvarmodule *cvmodule_in)
{
  const cvm::atom_pos pos1{a1x, a1y, a1z};
  const cvm::atom_pos pos2{a2x, a2y, a2z};
  cvm::rvector const diff = (flags & ef_use_internal_pbc)
                                ? cvmodule_in->proxy->position_distance_internal(pos1, pos2)
                                : cvmodule_in->proxy->position_distance(pos1, pos2);
 
  cvm::rvector const scal_diff(diff.x * inv_r0_vec.x,
                               diff.y * inv_r0_vec.y,
                               diff.z * inv_r0_vec.z);
  cvm::real const l2 = scal_diff.norm2();
  if (flags & ef_use_pairlist) {
    if (l2 > pairlist_tol_l2_max) {
      // Exit if the distance is such that F(l2) < pairlist_tol
      return 0.0;
    }
  }
 
  cvm::real dFdl2 = 0.0;
  cvm::real F = switching_function<flags>(l2, dFdl2, en, ed, pairlist_tol);
 
  if ((flags & ef_gradients) && (F > 0.0)) {
    cvm::rvector const dl2dx((2.0 * inv_r0sq_vec.x) * diff.x,
                             (2.0 * inv_r0sq_vec.y) * diff.y,
                             (2.0 * inv_r0sq_vec.z) * diff.z);
 
    const cvm::rvector G = dFdl2*dl2dx;
    g1x += -1.0*G.x;
    g1y += -1.0*G.y;
    g1z += -1.0*G.z;
    g2x +=      G.x;
    g2y +=      G.y;
    g2z +=      G.z;
  }
 
  return F;
}
 
#endif // COLVARCOMP_COORDNUM_H