ReferenceRbDihedralBond.cpp

/* Portions copyright (c) 2006-2016 Stanford University and Simbios.
 * Contributors: Pande Group
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#include <string.h>
#include <sstream>

#include "SimTKOpenMMUtilities.h"
#include "ReferenceRbDihedralBond.h"
#include "ReferenceForce.h"

using std::vector;
using namespace OpenMM;

/**---------------------------------------------------------------------------------------

   ReferenceRbDihedralBond constructor

   --------------------------------------------------------------------------------------- */

ReferenceRbDihedralBond::ReferenceRbDihedralBond() : usePeriodic(false) {
}

/**---------------------------------------------------------------------------------------

   ReferenceRbDihedralBond destructor

   --------------------------------------------------------------------------------------- */

ReferenceRbDihedralBond::~ReferenceRbDihedralBond() {
}

void ReferenceRbDihedralBond::setPeriodic(OpenMM::Vec3* vectors) {
    usePeriodic = true;
    boxVectors[0] = vectors[0];
    boxVectors[1] = vectors[1];
    boxVectors[2] = vectors[2];
}

/**---------------------------------------------------------------------------------------

   Calculate Ryckaert-Bellemans bond ixn

   @param atomIndices      atom indices of 4 atoms in bond
   @param atomCoordinates  atom coordinates
   @param parameters       six RB parameters
   @param forces           force array (forces added to current values)
   @param totalEnergy      if not null, the energy will be added to this

   --------------------------------------------------------------------------------------- */

void ReferenceRbDihedralBond::calculateBondIxn(vector<int>& atomIndices,
                                               vector<Vec3>& atomCoordinates,
                                               vector<double>& parameters,
                                               vector<Vec3>& forces,
                                               double* totalEnergy, double* energyParamDerivs) {
   // number of parameters

   static const int numberOfParameters = 6;

   double deltaR[3][ReferenceForce::LastDeltaRIndex];

   double crossProductMemory[6];

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

   // get deltaR, R2, and R between 2 atoms

   int atomAIndex = atomIndices[0];
   int atomBIndex = atomIndices[1];
   int atomCIndex = atomIndices[2];
   int atomDIndex = atomIndices[3];
   if (usePeriodic) {
      ReferenceForce::getDeltaRPeriodic(atomCoordinates[atomBIndex], atomCoordinates[atomAIndex], boxVectors, deltaR[0]);  
      ReferenceForce::getDeltaRPeriodic(atomCoordinates[atomBIndex], atomCoordinates[atomCIndex], boxVectors, deltaR[1]);  
      ReferenceForce::getDeltaRPeriodic(atomCoordinates[atomDIndex], atomCoordinates[atomCIndex], boxVectors, deltaR[2]);  
   }
   else {
      ReferenceForce::getDeltaR(atomCoordinates[atomBIndex], atomCoordinates[atomAIndex], deltaR[0]);  
      ReferenceForce::getDeltaR(atomCoordinates[atomBIndex], atomCoordinates[atomCIndex], deltaR[1]);  
      ReferenceForce::getDeltaR(atomCoordinates[atomDIndex], atomCoordinates[atomCIndex], deltaR[2]);  
   }

   double cosPhi;
   double signOfAngle;
   int hasREntry = 1;

   // Visual Studio complains if crossProduct declared as 'crossProduct[2][3]'

   double* crossProduct[2];
   crossProduct[0]           = crossProductMemory;
   crossProduct[1]           = crossProductMemory + 3;
   double dihederalAngle = getDihedralAngleBetweenThreeVectors(deltaR[0], deltaR[1], deltaR[2],
                                                               crossProduct, &cosPhi, deltaR[0], 
                                                               &signOfAngle, hasREntry);

   // Gromacs: use polymer convention

   if (dihederalAngle < 0.0) {
      dihederalAngle += PI_M;
   } else {
      dihederalAngle -= PI_M;
   }
   cosPhi *= -1.0;

   // Ryckaert-Bellemans:

   // V = sum over i: { C_i*cos(psi)**i }, where psi = phi - PI, 
   //                                              C_i is ith RB coefficient

   double dEdAngle       = 0.0;
   double energy         = parameters[0];
   double cosFactor      = 1.0;
   for (int ii = 1; ii < numberOfParameters; ii++) {
      dEdAngle  -= ii*parameters[ii]*cosFactor;
      cosFactor *= cosPhi;
      energy    += cosFactor*parameters[ii];
   }

   dEdAngle *= SIN(dihederalAngle);

   double internalF[4][3];
   double forceFactors[4];
   double normCross1         = DOT3(crossProduct[0], crossProduct[0]);
   double normBC             = deltaR[1][ReferenceForce::RIndex];
          forceFactors[0]    = (-dEdAngle*normBC)/normCross1;

   double normCross2         = DOT3(crossProduct[1], crossProduct[1]);
          forceFactors[3]    = (dEdAngle*normBC)/normCross2;

          forceFactors[1]    = DOT3(deltaR[0], deltaR[1]);
          forceFactors[1]   /= deltaR[1][ReferenceForce::R2Index];

          forceFactors[2]    = DOT3(deltaR[2], deltaR[1]);
          forceFactors[2]   /= deltaR[1][ReferenceForce::R2Index];

   for (int ii = 0; ii < 3; ii++) {

      internalF[0][ii]  = forceFactors[0]*crossProduct[0][ii];
      internalF[3][ii]  = forceFactors[3]*crossProduct[1][ii];

      double s          = forceFactors[1]*internalF[0][ii] - forceFactors[2]*internalF[3][ii]; 

      internalF[1][ii]  = internalF[0][ii] - s;
      internalF[2][ii]  = internalF[3][ii] + s;
   }

   // accumulate forces

   for (int ii = 0; ii < 3; ii++) {
      forces[atomAIndex][ii] += internalF[0][ii];
      forces[atomBIndex][ii] -= internalF[1][ii];
      forces[atomCIndex][ii] -= internalF[2][ii];
      forces[atomDIndex][ii] += internalF[3][ii];
   }

   // accumulate energies

   if (totalEnergy != NULL)
       *totalEnergy += energy;
}