charmmNonBonded.h

Go to the documentation of this file.

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

// Molecular Mechanics: Charmm force field, non-bonded component
// (van der Waals, electrostatics, EEF1 solvation)
//

#ifndef BALL_MOLMEC_CHARMM_NONBONDED_H
#define BALL_MOLMEC_CHARMM_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_PARAMETER_CHARMMEEF1_H
# include <BALL/MOLMEC/PARAMETER/charmmEEF1.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 BALL_EXPORT CharmmNonBonded 
    : public ForceFieldComponent
  {
    public:

    #define CHARMM_NB_ENABLED "enable NB"


    BALL_CREATE(CharmmNonBonded)

    
    CharmmNonBonded()
      ;

    CharmmNonBonded(ForceField& force_field)
      ;

    CharmmNonBonded(const CharmmNonBonded& charmm_non_bonded)
      ;

    virtual ~CharmmNonBonded()
      ;


    
    const CharmmNonBonded& operator = 
      (const CharmmNonBonded& charmm_non_bonded)
      ;

    virtual void clear()
      ;



    bool operator == (const CharmmNonBonded& charmm_non_bonded)
      ;



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



    virtual double updateEnergy()
      ;

    virtual void updateForces()
      ;

    virtual double getElectrostaticEnergy() const
      ;

    virtual double getVdwEnergy() const
      ;

    virtual double getSolvationEnergy() const
      ;



    virtual MolmecSupport::PairListAlgorithmType  
      determineMethodOfAtomPairGeneration()
      ;

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


    protected:

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

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

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

    /*_ Value of the solvation energy
    */
    double solvation_energy_;

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

    private:

    /*_ Vector array with all atom pairs whose distance is smaller than cut_off
    */
    vector<LennardJones::Data>  non_bonded_;
    
    /*_ A helper array for buildVectorOfNonBondedAtomPairs(). This is
        declared here to save the ctor within the method.
    */
    vector<bool> is_torsion_;

    /*_ Number of 1-4 interactions in the vector non_bonded
    */
    Size  number_of_1_4_; 

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

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

    /*_ Start of the switch function for the vdw interactions
    */
    float cut_on_vdw_;

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

    /*_ Start of the switch function for the vdw interactions
    */
    float cut_on_electrostatic_;

    /*_ Cutoff distance for solvation contribution (EEF1)
    */
    float cut_off_solvation_;

    /*_ Start of the switch function for the solvation contribution (EEF1)
    */
    float cut_on_solvation_;

    /*_ Inverse cube of the difference of cutoff and cuton for vdW
    */
    float inverse_difference_off_on_vdw_3_;

    /*_ Inverse cube of the difference of cutoff and cuton for solvation
    */
    float inverse_difference_off_on_solvation_3_;

    /*_ Inverse cube of the difference of cutoff and cuton for electrostatic
    */
    float inverse_difference_off_on_electrostatic_3_;

    /*_ Scaling factor for vdw_1_4_interactions
    */
    float scaling_vdw_1_4_;

    /*_ Scaling factor for electrostatic_1_4_interactions
    */
    float 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_parameters_;

    LennardJones                van_der_waals_parameters_14_;

    CharmmEEF1                  solvation_parameters_;

    vector<CharmmEEF1::Values>  solvation_;

    bool use_solvation_component_;

    //_@}

  };
} // namespace BALL

#endif // BALL_MOLMEC_CHARMM_CHARMMVDW_H