ReferenceGBVI.h

/* Portions copyright (c) 2006 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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 * permit persons to whom the Software is furnished to do so, subject
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 *
 * The above copyright notice and this permission notice shall be included
 * in all copies or substantial portions of the Software.
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 * OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
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 */

#ifndef __ReferenceGBVI_H__
#define __ReferenceGBVI_H__

#include <vector>

#include "RealVec.h"
#include "GBVIParameters.h"

namespace OpenMM {

class ReferenceGBVI {

   private:

      // GB/VI parameters

      GBVIParameters* _gbviParameters;
      std::vector<RealOpenMM> _switchDeriviative;

   public:

      /**---------------------------------------------------------------------------------------
      
         Constructor
      
         @param implicitSolventParameters    ImplicitSolventParameters reference
      
         @return CpuImplicitSolvent object
      
         --------------------------------------------------------------------------------------- */

       ReferenceGBVI(GBVIParameters* gbviParameters);

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

       ~ReferenceGBVI();

      /**---------------------------------------------------------------------------------------
      
         Return GBVIParameters
      
         @return GBVIParameters
      
         --------------------------------------------------------------------------------------- */

      GBVIParameters* getGBVIParameters() const;

      /**---------------------------------------------------------------------------------------
      
         Set ImplicitSolventParameters
      
         @param ImplicitSolventParameters
      
         --------------------------------------------------------------------------------------- */

      void setGBVIParameters(GBVIParameters* gbviParameters);
 
      /**---------------------------------------------------------------------------------------
      
         Get Born radii based on Eq. 3 of Labute paper [JCC 29 p. 1693-1698 2008])

         @param atomCoordinates   atomic coordinates
         @param bornRadii         output array of Born radii
         @param gbviChain         not used
      
         --------------------------------------------------------------------------------------- */
      
      void computeBornRadii(const std::vector<OpenMM::RealVec>& atomCoordinates, std::vector<RealOpenMM>& bornRadii);
      
      /**---------------------------------------------------------------------------------------
      
         Get volume Eq. 4 of Labute paper [JCC 29 p. 1693-1698 2008])
      
         @param r                   distance between atoms i & j
         @param R                   atomic radius
         @param S                   scaled atomic radius
      
         @return volume
      
         --------------------------------------------------------------------------------------- */
      
      static RealOpenMM getVolume(RealOpenMM r, RealOpenMM R, RealOpenMM S);
      
      /**---------------------------------------------------------------------------------------
      
         Get L (analytical solution for volume integrals) 
      
         @param r                   distance between atoms i & j
         @param R                   atomic radius
         @param S                   scaled atomic radius
      
         @return L value (Eq. 4 of Labute paper [JCC 29 p. 1693-1698 2008])
      
         --------------------------------------------------------------------------------------- */
      
      static RealOpenMM getL(RealOpenMM r, RealOpenMM x, RealOpenMM S);

      /**---------------------------------------------------------------------------------------
      
         Get partial derivative of L wrt r
      
         @param r                   distance between atoms i & j
         @param R                   atomic radius
         @param S                   scaled atomic radius
      
         @return partial derivative based on Eq. 4 of Labute paper [JCC 29 p. 1693-1698 2008])
      
         --------------------------------------------------------------------------------------- */
      
      static RealOpenMM dL_dr(RealOpenMM r, RealOpenMM x, RealOpenMM S);

      /**---------------------------------------------------------------------------------------
      
         Get partial derivative of L wrt x
      
         @param r                   distance between atoms i & j
         @param R                   atomic radius
         @param S                   scaled atomic radius
      
         @return partial derivative based on Eq. 4 of Labute paper [JCC 29 p. 1693-1698 2008])
      
         --------------------------------------------------------------------------------------- */
      
      static RealOpenMM dL_dx(RealOpenMM r, RealOpenMM x, RealOpenMM S);

      /**---------------------------------------------------------------------------------------
      
         Sgb function
      
         @param t                   r*r*G_i*G_j
      
         @return Sgb (p. 1694 of Labute paper [JCC 29 p. 1693-1698 2008])
      
         --------------------------------------------------------------------------------------- */
      
      static RealOpenMM Sgb(RealOpenMM t);
      
      /**---------------------------------------------------------------------------------------
      
         Get GB/VI energy
      
         @param atomCoordinates     atomic coordinates
         @param partialCharges      partial charges
      
         @return energy
      
         --------------------------------------------------------------------------------------- */
      
      RealOpenMM computeBornEnergy(const std::vector<OpenMM::RealVec>& atomCoordinates, const std::vector<RealOpenMM>& partialCharges);
      
      /**---------------------------------------------------------------------------------------
      
         Get GB/VI forces
      
         @param atomCoordinates     atomic coordinates
         @param partialCharges      partial charges
         @param forces              output forces
      
         --------------------------------------------------------------------------------------- */
      
      void computeBornForces(std::vector<OpenMM::RealVec>& atomCoordinates,
                             const std::vector<RealOpenMM>& partialCharges, std::vector<OpenMM::RealVec>& inputForces);
      
      /**---------------------------------------------------------------------------------------
      
         Get volume Eq. 4 of Labute paper [JCC 29 p. 1693-1698 2008])
      
         @param r                   distance between atoms i & j
         @param R                   atomic radius
         @param S                   scaled atomic radius
      
         @return volume
      
         --------------------------------------------------------------------------------------- */
      
      static double getVolumeD(double r, double R, double S);
      
      /**---------------------------------------------------------------------------------------
      
         Get L (analytical solution for volume integrals) 
      
         @param r                   distance between atoms i & j
         @param R                   atomic radius
         @param S                   scaled atomic radius
      
         @return L value (Eq. 4 of Labute paper [JCC 29 p. 1693-1698 2008])
      
         --------------------------------------------------------------------------------------- */
      
      static double getLD(double r, double x, double S);

      /**---------------------------------------------------------------------------------------
      
         Get partial derivative of L wrt r
      
         @param r                   distance between atoms i & j
         @param R                   atomic radius
         @param S                   scaled atomic radius
      
         @return partial derivative based on Eq. 4 of Labute paper [JCC 29 p. 1693-1698 2008])
      
         --------------------------------------------------------------------------------------- */
      
      static double dL_drD(double r, double x, double S);

      /**---------------------------------------------------------------------------------------
      
         Get partial derivative of L wrt x
      
         @param r                   distance between atoms i & j
         @param R                   atomic radius
         @param S                   scaled atomic radius
      
         @return partial derivative based on Eq. 4 of Labute paper [JCC 29 p. 1693-1698 2008])
      
         --------------------------------------------------------------------------------------- */
      
      static double dL_dxD(double r, double x, double S);

    /**---------------------------------------------------------------------------------------
    
       Return OBC chain derivative: size = _obcParameters->getNumberOfAtoms()
       On first call, memory for array is allocated if not set
    
       @return array
    
       --------------------------------------------------------------------------------------- */
    
      std::vector<RealOpenMM>& getSwitchDeriviative();
    
    /**---------------------------------------------------------------------------------------
    
       Compute quintic spline value and associated derviative
    
       @param x                   value to compute spline at
       @param rl                  lower cutoff value
       @param ru                  upper cutoff value
       @param outValue            value of spline at x
       @param outDerivative       value of derivative of spline at x
    
       --------------------------------------------------------------------------------------- */
    
    void quinticSpline(RealOpenMM x, RealOpenMM rl, RealOpenMM ru,
                       RealOpenMM* outValue, RealOpenMM* outDerivative);

    /**---------------------------------------------------------------------------------------
    
       Compute Born radii based on Eq. 3 of Labute paper [JCC 29 p. 1693-1698 2008])
       and quintic splice switching function
    
       @param atomicRadius3       atomic radius cubed
       @param bornSum             Born sum (volume integral)
       @param gbviParameters      Gbvi parameters (parameters used in spline
                                  QuinticLowerLimitFactor & QuinticUpperBornRadiusLimit)
       @param bornRadius          output Born radius
       @param switchDeriviative   output switching function deriviative
    
       --------------------------------------------------------------------------------------- */
    
    void computeBornRadiiUsingQuinticSpline(RealOpenMM atomicRadius3, RealOpenMM bornSum,
                                            GBVIParameters* gbviParameters,
                                            RealOpenMM* bornRadius, RealOpenMM* switchDeriviative);

};

} // namespace OpenMM

#endif // __ReferenceGBVI_H__