charmmNonBonded.h

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// -*- 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();



    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);

 
    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