amberNonBonded.h

Go to the documentation of this file.

// -*- Mode: C++; tab-width: 2; -*-
// vi: set ts=2:
//

// Molecular Mechanics: Amber force field, non-bonded component

#ifndef BALL_MOLMEC_AMBER_NONBONDED_H
#define BALL_MOLMEC_AMBER_NONBONDED_H

#ifndef BALL_COMMON_H
# include <BALL/common.h>
#endif

#ifndef BALL_MOLMEC_PARAMETER_LENNARDJONES_H
# include <BALL/MOLMEC/PARAMETER/lennardJones.h>
#endif

#ifndef BALL_MOLMEC_PARAMETER_POTENTIAL1210_H
# include <BALL/MOLMEC/PARAMETER/potential1210.h>
#endif

#ifndef BALL_MOLMEC_COMMON_FORCEFIELDCOMPONENT_H
# include <BALL/MOLMEC/COMMON/forceFieldComponent.h>
#endif

#ifndef BALL_MOLMEC_COMMON_SUPPORT_H
# include <BALL/MOLMEC/COMMON/support.h>
#endif

namespace BALL 
{
  class AdvancedElectrostatic;

  class BALL_EXPORT AmberNonBonded 
    : public ForceFieldComponent
  {
    public:

    #define AMBER_NB_ENABLED "enable NB"

    // NA*e0*e0*1e7 / (4.0*PI*VACUUM_PERMITTIVITY)
    static const double ELECTROSTATIC_FACTOR;


    BALL_CREATE(AmberNonBonded)

    
    AmberNonBonded()
      ;

    AmberNonBonded(ForceField& force_field)
      ;

    AmberNonBonded(const AmberNonBonded& amber_non_bonded)
      ;

    virtual ~AmberNonBonded()
      ;

    
    const AmberNonBonded& operator = (const AmberNonBonded& anb)
      ;

    virtual void clear()
      ;


      
    bool operator == (const AmberNonBonded& anb)
      ;



    virtual bool setup()
      throw(Exception::TooManyErrors);


    bool setup(Options& options, ForceFieldParameters& par);




    virtual double updateEnergy()
      ;

    virtual void updateForces()
      ;

    virtual void update()
      throw(Exception::TooManyErrors);


    void update(const std::vector<std::pair<Atom*, Atom*> >& atom_vector);


    virtual double getElectrostaticEnergy() const
      ;

    virtual double getVdwEnergy() const
      ;



    virtual MolmecSupport::PairListAlgorithmType
      determineMethodOfAtomPairGeneration()
      ;

    virtual void buildVectorOfNonBondedAtomPairs
      (const std::vector<std::pair<Atom*, Atom*> >& atom_vector,
       const LennardJones& lennard_jones,
       const Potential1210& hydrogen_bond)
      throw(Exception::TooManyErrors);


    void enableStoreInteractions(bool b=true);

    void setAdvancedElectrostatic(AdvancedElectrostatic* advES);

    protected:

    /*_ @name Protected Attributes  
    */
    //_@{

    /*_ Value of the electrostatic energy
    */
    double  electrostatic_energy_;

    /*_ Value of the vdw energy
    */
    double  vdw_energy_;

    //_@}

    private:

    /*_ @name Private Attributes  
    */
    //_@{

    /*_ Vector array with all atom pairs whose distance is smaller than cut_off
    */
    std::vector<LennardJones::Data> non_bonded_;

    /*_ Vector of flags deciding whether the pair forms a hydrogen bond or a
        standard VdW interaction.
    */
    std::vector<char> is_hydrogen_bond_;
 
    /*_ Number of 1-4 interactions in the vector non_bonded
    */
    Size  number_of_1_4_; 

    /*_ Number of hydrogen bond interactions in the vector non_bonded
    */
    Size  number_of_h_bonds_; 

    /*_ Cutoff distance for non-bonded interactions
    */
    double  cut_off_;

    /*_ Cutoff distance for vdw interactions
    */
    double  cut_off_vdw_;

    /*_ Cuton distance for vdw interactions
    */
    double  cut_on_vdw_;

    /*_ Cutoff distance for electrostatic interactions
    */
    double  cut_off_electrostatic_;

    /*_ Cuton distance for electrostatic interactions
    */
    double  cut_on_electrostatic_;

    /*_ Inverse cube of the difference of squares of cuton and cutoff for vdW.
        This value is required for the switching function
    */
    double inverse_distance_off_on_vdw_3_;
    
    /*_ Inverse cube of the difference of squares of cuton and cutoff for eletrostatic.
        This value is required for the switching function
    */
    double inverse_distance_off_on_electrostatic_3_;
    
    /*_ Scaling factor for vdw_1_4_interactions
    */
    double  scaling_vdw_1_4_;

    /*_ Scaling factor for electrostatic_1_4_interactions
    */
    double  scaling_electrostatic_1_4_;

    /*_ Flag for using constant or distance dependent dielectric constant.
        True = distance dependent
    */
    bool    use_dist_depend_dielectric_; 

    /*_ The most efficient algorithm to calculate the non-bonded atom pairs.
        {\tt BRUTE\_FORCE}: brute force: all against all\\
        {\tt HASH\_GRID}: box grid
    */
    MolmecSupport::PairListAlgorithmType  algorithm_type_;
    
    LennardJones  van_der_waals_;

    Potential1210 hydrogen_bond_;

    //_@}

  };
} // namespace BALL

#endif // BALL_MOLMEC_AMBER_AMBERVDW_H