nonbonded_interaction_data.hpp

Go to the documentation of this file.

/*
 * Copyright (C) 2010-2026 The ESPResSo project
 * Copyright (C) 2002,2003,2004,2005,2006,2007,2008,2009,2010
 *   Max-Planck-Institute for Polymer Research, Theory Group
 *
 * This file is part of ESPResSo.
 *
 * ESPResSo is free software: you can redistribute it and/or modify
 * it under the terms of the GNU General Public License as published by
 * the Free Software Foundation, either version 3 of the License, or
 * (at your option) any later version.
 *
 * ESPResSo is distributed in the hope that it will be useful,
 * but WITHOUT ANY WARRANTY; without even the implied warranty of
 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
 * GNU General Public License for more details.
 *
 * You should have received a copy of the GNU General Public License
 * along with this program.  If not, see <http://www.gnu.org/licenses/>.
 */
 
#pragma once
 
/** \file
 *  Various procedures concerning interactions between particles.
 */
 
#include <config/config.hpp>
 
#include "TabulatedPotential.hpp"
#include "system/Leaf.hpp"
 
#include <utils/index.hpp>
#include <utils/math/int_pow.hpp>
 
#include <algorithm>
#include <cassert>
#include <cmath>
#include <memory>
#include <vector>
 
/** Lennard-Jones with shift */
struct LJ_Parameters {
  double eps = 0.0;
  double sig = 0.0;
  double cut = inactive_cutoff;
  double shift = 0.0;
  double offset = 0.0;
  double min = 0.0;
  LJ_Parameters() = default;
  LJ_Parameters(double epsilon, double sigma, double cutoff, double offset,
                double min, double shift);
  double get_auto_shift() const {
    auto auto_shift = 0.;
    if (cut != 0.) {
      auto_shift = Utils::int_pow<6>(sig / cut) - Utils::int_pow<12>(sig / cut);
    }
    return auto_shift;
  }
  double max_cutoff() const { return cut + offset; }
  double min_cutoff() const { return min + offset; }
};
 
/** WCA potential */
struct WCA_Parameters {
  double eps = 0.0;
  double sig = 0.0;
  double cut = inactive_cutoff;
  WCA_Parameters() = default;
  WCA_Parameters(double epsilon, double sigma);
  double max_cutoff() const { return cut; }
};
 
/** Generic Lennard-Jones with shift */
struct LJGen_Parameters {
  double eps = 0.0;
  double sig = 0.0;
  double cut = inactive_cutoff;
  double shift = 0.0;
  double offset = 0.0;
  double lambda = 1.0;
  double softrad = 0.0;
  double a1 = 0.0;
  double a2 = 0.0;
  double b1 = 0.0;
  double b2 = 0.0;
  LJGen_Parameters() = default;
  LJGen_Parameters(double epsilon, double sigma, double cutoff, double shift,
                   double offset,
#ifdef ESPRESSO_LJGEN_SOFTCORE
                   double lam, double delta,
#endif
                   double e1, double e2, double b1, double b2);
  double get_auto_shift() const {
    auto auto_shift = 0.;
    if (cut != 0.) {
      auto_shift = b2 * std::pow(sig / cut, a2) - b1 * std::pow(sig / cut, a1);
    }
    return auto_shift;
  }
  double max_cutoff() const { return cut + offset; }
};
 
/** smooth step potential */
struct SmoothStep_Parameters {
  double eps = 0.0;
  double sig = 0.0;
  double cut = inactive_cutoff;
  double d = 0.0;
  int n = 0;
  double k0 = 0.0;
  SmoothStep_Parameters() = default;
  SmoothStep_Parameters(double eps, double sig, double cutoff, double d, int n,
                        double k0);
  double max_cutoff() const { return cut; }
};
 
/** Hertzian potential */
struct Hertzian_Parameters {
  double eps = 0.0;
  double sig = inactive_cutoff;
  Hertzian_Parameters() = default;
  Hertzian_Parameters(double eps, double sig);
  double max_cutoff() const { return sig; }
};
 
/** Gaussian potential */
struct Gaussian_Parameters {
  double eps = 0.0;
  double sig = 1.0;
  double cut = inactive_cutoff;
  Gaussian_Parameters() = default;
  Gaussian_Parameters(double eps, double sig, double cutoff);
  double max_cutoff() const { return cut; }
};
 
/** BMHTF NaCl potential */
struct BMHTF_Parameters {
  double A = 0.0;
  double B = 0.0;
  double C = 0.0;
  double D = 0.0;
  double sig = 0.0;
  double cut = inactive_cutoff;
  double computed_shift = 0.0;
  BMHTF_Parameters() = default;
  BMHTF_Parameters(double A, double B, double C, double D, double sig,
                   double cut);
  double max_cutoff() const { return cut; }
};
 
/** Morse potential */
struct Morse_Parameters {
  double eps = 0.;
  double alpha = inactive_cutoff;
  double rmin = inactive_cutoff;
  double cut = inactive_cutoff;
  double rest = inactive_cutoff;
  Morse_Parameters() = default;
  Morse_Parameters(double eps, double alpha, double rmin, double cutoff);
  double max_cutoff() const { return cut; }
};
 
/** Buckingham potential */
struct Buckingham_Parameters {
  double A = 0.0;
  double B = 0.0;
  double C = 0.0;
  double D = 0.0;
  double cut = inactive_cutoff;
  double discont = 0.0;
  double shift = 0.0;
  double F1 = 0.0;
  double F2 = 0.0;
  Buckingham_Parameters() = default;
  Buckingham_Parameters(double a, double b, double c, double d, double cutoff,
                        double discont, double shift);
  double max_cutoff() const { return cut; }
};
 
/** soft-sphere potential */
struct SoftSphere_Parameters {
  double a = 0.0;
  double n = 0.0;
  double cut = inactive_cutoff;
  double offset = 0.0;
  SoftSphere_Parameters() = default;
  SoftSphere_Parameters(double a, double n, double cutoff, double offset);
  double max_cutoff() const { return cut + offset; }
};
 
/** hat potential */
struct Hat_Parameters {
  double Fmax = 0.0;
  double r = inactive_cutoff;
  Hat_Parameters() = default;
  Hat_Parameters(double F_max, double cutoff);
  double max_cutoff() const { return r; }
};
 
/** Lennard-Jones+Cos potential */
struct LJcos_Parameters {
  double eps = 0.0;
  double sig = 0.0;
  double cut = inactive_cutoff;
  double offset = 0.0;
  double alfa = 0.0;
  double beta = 0.0;
  double rmin = 0.0;
  LJcos_Parameters() = default;
  LJcos_Parameters(double epsilon, double sigma, double cutoff, double offset);
  double max_cutoff() const { return cut + offset; }
};
 
/** Lennard-Jones with a different Cos potential */
struct LJcos2_Parameters {
  double eps = 0.0;
  double sig = 0.0;
  double cut = inactive_cutoff;
  double offset = 0.0;
  double w = 0.0;
  double rchange = 0.0;
  LJcos2_Parameters() = default;
  LJcos2_Parameters(double epsilon, double sigma, double offset, double width);
  double max_cutoff() const { return cut + offset; }
};
 
/** Gay-Berne potential */
struct GayBerne_Parameters {
  double eps = 0.0;
  double sig = 0.0;
  double cut = inactive_cutoff;
  double k1 = 0.0;
  double k2 = 0.0;
  double mu = 0.0;
  double nu = 0.0;
  double chi1 = 0.0;
  double chi2 = 0.0;
  GayBerne_Parameters() = default;
  GayBerne_Parameters(double eps, double sig, double cut, double k1, double k2,
                      double mu, double nu);
  double max_cutoff() const { return cut; }
};
 
/** Thole potential */
struct Thole_Parameters {
  double scaling_coeff = 0.; // inactive cutoff is 0
  double q1q2 = 0.;
  Thole_Parameters() = default;
  Thole_Parameters(double scaling_coeff, double q1q2)
      : scaling_coeff{scaling_coeff}, q1q2{q1q2} {}
};
 
/** DPD potential */
struct DPDParameters {
  double gamma = 0.;
  double k = 1.;
  double cutoff = inactive_cutoff;
  int wf = 0;
  double pref = 0.0;
};
 
struct DPD_Parameters {
  DPDParameters radial;
  DPDParameters trans;
  DPD_Parameters() = default;
  DPD_Parameters(double gamma, double k, double r_c, int wf, double tgamma,
                 double tr_c, int twf) {
    radial = DPDParameters{gamma, k, r_c, wf, -1.};
    trans = DPDParameters{tgamma, k, tr_c, twf, -1.};
  }
  double max_cutoff() const { return std::max(radial.cutoff, trans.cutoff); }
};
 
/** @brief Bit positions in IA_parameters::active_pair_mask.
 *
 *  Each enumerator corresponds to one short-range pair potential
 *  (central-radial, orientation-dependent, or thermostat-coupled)
 *  configurable per type pair. A bit is set iff the potential's own
 *  cutoff / activation guard could possibly fire for this type pair
 *  (i.e. it is not in its default/inactive state). Populated
 *  exclusively by InteractionsNonBonded::recalc_maximal_cutoffs() —
 *  never set elsewhere, so it cannot drift from max_cut.
 */
enum class PairPotential : unsigned {
  LennardJones = 0,
  WCA,
  LennardJonesGeneric,
  SmoothStep,
  Hertzian,
  Gaussian,
  BMHTF,
  Buckingham,
  Morse,
  SoftSphere,
  Hat,
  LJCos,
  LJCos2,
  Tabulated,
  GayBerne,
  DPD,
};
 
/** @brief Bitmask for a pair potential. */
constexpr unsigned pair_potential_bit(PairPotential p) {
  return 1u << static_cast<unsigned>(p);
}
 
/** @brief Parameters for non-bonded interactions. */
struct IA_parameters {
  /** maximal cutoff for this pair of particle types. This contains
   *  contributions from the short-ranged interactions, plus any
   *  cutoffs from global interactions like electrostatics.
   */
  double max_cut = inactive_cutoff;
 
  /** Bitmask of pair potentials active for this type pair.
   *  See PairPotential. Derived, do not set directly.
   */
  unsigned active_pair_mask = 0u;
 
#ifdef ESPRESSO_LENNARD_JONES
  LJ_Parameters lj;
#endif
 
#ifdef ESPRESSO_WCA
  WCA_Parameters wca;
#endif
 
#ifdef ESPRESSO_LENNARD_JONES_GENERIC
  LJGen_Parameters ljgen;
#endif
 
#ifdef ESPRESSO_SMOOTH_STEP
  SmoothStep_Parameters smooth_step;
#endif
 
#ifdef ESPRESSO_HERTZIAN
  Hertzian_Parameters hertzian;
#endif
 
#ifdef ESPRESSO_GAUSSIAN
  Gaussian_Parameters gaussian;
#endif
 
#ifdef ESPRESSO_BMHTF_NACL
  BMHTF_Parameters bmhtf;
#endif
 
#ifdef ESPRESSO_MORSE
  Morse_Parameters morse;
#endif
 
#ifdef ESPRESSO_BUCKINGHAM
  Buckingham_Parameters buckingham;
#endif
 
#ifdef ESPRESSO_SOFT_SPHERE
  SoftSphere_Parameters soft_sphere;
#endif
 
#ifdef ESPRESSO_HAT
  Hat_Parameters hat;
#endif
 
#ifdef ESPRESSO_LJCOS
  LJcos_Parameters ljcos;
#endif
 
#ifdef ESPRESSO_LJCOS2
  LJcos2_Parameters ljcos2;
#endif
 
#ifdef ESPRESSO_GAY_BERNE
  GayBerne_Parameters gay_berne;
#endif
 
#ifdef ESPRESSO_TABULATED
  TabulatedPotential tab;
#endif
 
#ifdef ESPRESSO_DPD
  DPD_Parameters dpd;
#endif
 
#ifdef ESPRESSO_THOLE
  Thole_Parameters thole;
#endif
};
 
class InteractionsNonBonded : public System::Leaf<InteractionsNonBonded> {
  /** @brief List of pairwise interactions. */
  std::vector<std::shared_ptr<IA_parameters>> m_nonbonded_ia_params{};
  /** @brief Maximal particle type seen so far. */
  int max_seen_particle_type = -1;
 
  void realloc_ia_params(int type) {
    assert(type >= 0);
    auto const old_size = m_nonbonded_ia_params.size();
    m_nonbonded_ia_params.resize(Utils::lower_triangular(type, type) + 1);
    auto const new_size = m_nonbonded_ia_params.size();
    if (new_size > old_size) {
      for (auto &data : m_nonbonded_ia_params) {
        if (data == nullptr) {
          data = std::make_shared<IA_parameters>();
        }
      }
    }
  }
 
public:
  InteractionsNonBonded() {
    /* make sure interaction 0<->0 always exists */
    make_particle_type_exist(0);
  }
 
  /**
   * @brief Make sure the interaction parameter list is large enough to cover
   * interactions for this particle type.
   * New interactions are initialized with values such that no physical
   * interaction occurs.
   */
  void make_particle_type_exist(int type) {
    assert(type >= 0);
    if (type > max_seen_particle_type) {
      realloc_ia_params(type);
      max_seen_particle_type = type;
    }
  }
 
  auto get_ia_param_key(int i, int j) const {
    assert(i >= 0 and i <= max_seen_particle_type);
    assert(j >= 0 and j <= max_seen_particle_type);
    auto const key = static_cast<unsigned int>(
        Utils::lower_triangular(std::max(i, j), std::min(i, j)));
    assert(key < m_nonbonded_ia_params.size());
    return key;
  }
 
  /**
   * @brief Get interaction parameters between particle types i and j
   *
   * This is symmetric, e.g. it holds that `get_ia_param(i, j)` and
   * `get_ia_param(j, i)` point to the same data.
   *
   * @param i First type, must exist
   * @param j Second type, must exist
   *
   * @return Reference to interaction parameters for the type pair.
   */
  auto &get_ia_param(int i, int j) {
    return *m_nonbonded_ia_params[get_ia_param_key(i, j)];
  }
 
  auto const &get_ia_param(int i, int j) const {
    return *m_nonbonded_ia_params[get_ia_param_key(i, j)];
  }
 
  auto get_ia_param_ref_counted(int i, int j) const {
    return m_nonbonded_ia_params[get_ia_param_key(i, j)];
  }
 
  void set_ia_param(int i, int j, std::shared_ptr<IA_parameters> const &ia) {
    m_nonbonded_ia_params[get_ia_param_key(i, j)] = ia;
  }
 
  auto get_max_seen_particle_type() const { return max_seen_particle_type; }
 
  /** @brief Recalculate cutoff of each interaction struct. */
  void recalc_maximal_cutoffs();
 
  /** @brief Get maximal cutoff. */
  double maximal_cutoff() const;
 
  /** @brief Notify system that non-bonded interactions changed. */
  void on_non_bonded_ia_change() const;
 
#ifdef ESPRESSO_DPD
  void dpd_init(double kT, double time_step);
#endif
};