LennardJonesPairScore.h

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/**
 *  \file IMP/atom/LennardJonesPairScore.h
 *  \brief Lennard-Jones score between a pair of particles.
 *
 *  Copyright 2007-2022 IMP Inventors. All rights reserved.
 */

#ifndef IMPATOM_LENNARD_JONES_PAIR_SCORE_H
#define IMPATOM_LENNARD_JONES_PAIR_SCORE_H

#include <IMP/atom/atom_config.h>
#include <IMP/generic.h>
#include <IMP/PairScore.h>
#include <IMP/Pointer.h>
#include <IMP/atom/LennardJones.h>
#include <IMP/atom/smoothing_functions.h>

IMPATOM_BEGIN_NAMESPACE

//! Lennard-Jones score between a pair of particles.
/** The two particles in the pair must be LennardJones particles.
    The form of the potential is \f[
       -\epsilon \left[ w_{rep} \left(\frac{r_{min}}{r}\right)^{12}
                       - 2 w_{att} \left(\frac{r_{min}}{r}\right)^{6}\right]
    \f] where \f$\epsilon\f$ is the depth of the well between the
    two particles, \f$r_{min}\f$ the sum of the particles' radii, \f$r\f$
    the inter-particle distance, and \f$w_{rep}\f$ and \f$w_{att}\f$ the
    weights on the repulsive and attractive parts of the potential respectively;
    both weights are 1.0 by default.

    The well depth is the geometric mean of the individual particles' well
    depths (as extracted by LennardJones::get_well_depth).

    Note that because this score uses radii and well depths set in the particles
    themselves, the strength of the interaction cannot be changed for a
    particular pair of atoms (as is done in the CHARMM forcefield with the
    rarely-used NBFIX directive, for example). If the well depth or radius of
    a single particle is modified, that will affect its interaction with all
    particles.

    It is recommended that new code instead uses LennardJonesTypedPairScore,
    which is about twice as fast and can support NBFIX.
 */
class IMPATOMEXPORT LennardJonesPairScore : public PairScore {
  IMP::PointerMember<SmoothingFunction> smoothing_function_;
  double repulsive_weight_, attractive_weight_;

  // Calculate A, B factors from particle well depths and radii
  // It may be appropriate to cache these for speed since the particle
  // attributes rarely change and square roots are expensive
  inline void get_factors(const LennardJones &lj0, const LennardJones &lj1,
                          double &A, double &B) const {
    double well_depth = std::sqrt(lj0.get_well_depth() * lj1.get_well_depth());
    double rmin = lj0.get_radius() + lj1.get_radius();
    // probably faster than pow(rmin, 6) on systems that don't
    // have pow(double, int)
    double rmin6 = rmin * rmin * rmin * rmin * rmin * rmin;
    double rmin12 = rmin6 * rmin6;

    A = well_depth * rmin12 * repulsive_weight_;
    B = 2.0 * well_depth * rmin6 * attractive_weight_;
  }

 public:
  IMPATOM_DEPRECATED_OBJECT_DECL(2.23)
  LennardJonesPairScore(SmoothingFunction *f)
      : smoothing_function_(f),
        repulsive_weight_(1.0),
        attractive_weight_(1.0) {
    IMPATOM_DEPRECATED_OBJECT_DEF(
                 2.23, "Use LennardJonesTypedPairScore instead");
  }

  void set_repulsive_weight(double repulsive_weight) {
    repulsive_weight_ = repulsive_weight;
  }

  double get_repulsive_weight() const { return repulsive_weight_; }

  void set_attractive_weight(double attractive_weight) {
    attractive_weight_ = attractive_weight;
  }

  double get_attractive_weight() const { return attractive_weight_; }

  virtual double evaluate_index(Model *m,
                                const ParticleIndexPair &p,
                                DerivativeAccumulator *da) const override;
  virtual ModelObjectsTemp do_get_inputs(
      Model *m, const ParticleIndexes &pis) const override;
  IMP_PAIR_SCORE_METHODS(LennardJonesPairScore);
  IMP_OBJECT_METHODS(LennardJonesPairScore);
  ;
};

IMP_OBJECTS(LennardJonesPairScore, LennardJonesPairScores);

IMPATOM_END_NAMESPACE

#endif /* IMPATOM_LENNARD_JONES_PAIR_SCORE_H */