CpuNonbondedForce.h

/* Portions copyright (c) 2006-2013 Stanford University and Simbios.
 * Contributors: Pande Group
 *
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 * a copy of this software and associated documentation files (the
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 * distribute, sublicense, and/or sell copies of the Software, and to
 * permit persons to whom the Software is furnished to do so, subject
 * to the following conditions:
 *
 * The above copyright notice and this permission notice shall be included
 * in all copies or substantial portions of the Software.
 *
 * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS
 * OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
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#ifndef OPENMM_CPU_NONBONDED_FORCE_H__
#define OPENMM_CPU_NONBONDED_FORCE_H__

#include "ReferencePairIxn.h"
#include <set>
#include <utility>
#include <vector>
// ---------------------------------------------------------------------------------------

class CpuNonbondedForce {

   private:
       
      bool cutoff;
      bool useSwitch;
      bool periodic;
      bool ewald;
      bool pme;
      const std::vector<std::pair<int, int> >* neighborList;
      float periodicBoxSize[3];
      float cutoffDistance, switchingDistance;
      float krf, crf;
      float alphaEwald;
      int numRx, numRy, numRz;
      int meshDim[3];

      // parameter indices

      static const int SigIndex = 0;
      static const int EpsIndex = 1;
      static const int   QIndex = 2;
            
      /**---------------------------------------------------------------------------------------
      
         Calculate LJ Coulomb pair ixn between two atoms
      
         @param atom1            the index of the first atom
         @param atom2            the index of the second atom
         @param atomCoordinates  atom coordinates
         @param atomParameters   atom parameters (charges, c6, c12, ...)     atomParameters[atomIndex][paramterIndex]
         @param forces           force array (forces added)
         @param totalEnergy      total energy
            
         --------------------------------------------------------------------------------------- */
          
      void calculateOneIxn( int atom1, int atom2, float* atomCoordinates,
                            float** atomParameters, float* forces,
                            float* totalEnergy ) const;


   public:

      /**---------------------------------------------------------------------------------------
      
         Constructor
      
         --------------------------------------------------------------------------------------- */

       CpuNonbondedForce( );

      /**---------------------------------------------------------------------------------------
      
         Destructor
      
         --------------------------------------------------------------------------------------- */

       ~CpuNonbondedForce( );

      /**---------------------------------------------------------------------------------------
      
         Set the force to use a cutoff.
      
         @param distance            the cutoff distance
         @param neighbors           the neighbor list to use
         @param solventDielectric   the dielectric constant of the bulk solvent
      
         --------------------------------------------------------------------------------------- */
      
      void setUseCutoff( float distance, const std::vector<std::pair<int, int> >& neighbors, float solventDielectric );

      /**---------------------------------------------------------------------------------------
      
         Set the force to use a switching function on the Lennard-Jones interaction.
      
         @param distance            the switching distance
      
         --------------------------------------------------------------------------------------- */
      
      void setUseSwitchingFunction( float distance );
      
      /**---------------------------------------------------------------------------------------
      
         Set the force to use periodic boundary conditions.  This requires that a cutoff has
         already been set, and the smallest side of the periodic box is at least twice the cutoff
         distance.
      
         @param boxSize             the X, Y, and Z widths of the periodic box
      
         --------------------------------------------------------------------------------------- */
      
      void setPeriodic( float* boxSize );
       
      /**---------------------------------------------------------------------------------------
      
         Set the force to use Ewald summation.
      
         @param alpha  the Ewald separation parameter
         @param kmaxx  the largest wave vector in the x direction
         @param kmaxy  the largest wave vector in the y direction
         @param kmaxz  the largest wave vector in the z direction
      
         --------------------------------------------------------------------------------------- */
      
      void setUseEwald(float alpha, int kmaxx, int kmaxy, int kmaxz);

     
      /**---------------------------------------------------------------------------------------
      
         Set the force to use Particle-Mesh Ewald (PME) summation.
      
         @param alpha    the Ewald separation parameter
         @param gridSize the dimensions of the mesh
      
         --------------------------------------------------------------------------------------- */
      
      void setUsePME(float alpha, int meshSize[3]);
      
      /**---------------------------------------------------------------------------------------
      
         Calculate LJ Coulomb pair ixn
      
         @param numberOfAtoms    number of atoms
         @param atomCoordinates  atom coordinates
         @param atomParameters   atom parameters (charges, c6, c12, ...)     atomParameters[atomIndex][paramterIndex]
         @param exclusions       atom exclusion indices
                                 exclusions[atomIndex] contains the list of exclusions for that atom
         @param fixedParameters  non atom parameters (not currently used)
         @param forces           force array (forces added)
         @param totalEnergy      total energy
         @param includeDirect      true if direct space interactions should be included
         @param includeReciprocal  true if reciprocal space interactions should be included
      
         --------------------------------------------------------------------------------------- */
          
      void calculatePairIxn(int numberOfAtoms, float* atomCoordinates,
                            float** atomParameters, std::vector<std::set<int> >& exclusions,
                            float* fixedParameters, float* forces,
                            float* totalEnergy, bool includeDirect, bool includeReciprocal) const;

private:
      /**---------------------------------------------------------------------------------------
      
         Calculate Ewald ixn
      
         @param numberOfAtoms    number of atoms
         @param atomCoordinates  atom coordinates
         @param atomParameters   atom parameters (charges, c6, c12, ...)     atomParameters[atomIndex][paramterIndex]
         @param exclusions       atom exclusion indices
                                 exclusions[atomIndex] contains the list of exclusions for that atom
         @param fixedParameters  non atom parameters (not currently used)
         @param forces           force array (forces added)
         @param totalEnergy      total energy
         @param includeDirect      true if direct space interactions should be included
         @param includeReciprocal  true if reciprocal space interactions should be included
            
         --------------------------------------------------------------------------------------- */
          
      void calculateEwaldIxn(int numberOfAtoms, float* atomCoordinates,
                            float** atomParameters, std::vector<std::set<int> >& exclusions,
                            float* fixedParameters, float* forces,
                            float* totalEnergy, bool includeDirect, bool includeReciprocal) const;
      
      void getDeltaR(const float* atomCoordinatesI, const float* atomCoordinatesJ,
                               const float* boxSize, float* deltaR, bool periodic) const;

};

// ---------------------------------------------------------------------------------------

#endif // OPENMM_CPU_NONBONDED_FORCE_H__