ReferenceAngleBondIxn.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 "ReferenceAngleBondIxn.h"
#include "ReferenceForce.h"

using std::vector;
using namespace OpenMM;

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

   ReferenceAngleBondIxn constructor

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

ReferenceAngleBondIxn::ReferenceAngleBondIxn() : usePeriodic(false) {
}

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

   ReferenceAngleBondIxn destructor

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

ReferenceAngleBondIxn::~ReferenceAngleBondIxn() {
}

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

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

   Get dEdR and energy term for angle bond

   @param  cosine               cosine of angle
   @param  angleParameters      angleParameters: angleParameters[0] = angle in radians
                                                 angleParameters[1] = k (force constant)
   @param  dEdR                 output dEdR
   @param  energyTerm           output energyTerm

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

void ReferenceAngleBondIxn::getPrefactorsGivenAngleCosine(double cosine, vector<double>& angleParameters,
                                                          double* dEdR, double* energyTerm) const {

   double angle;
   if (cosine >= 1.0) {
      angle = 0.0;
   } else if (cosine <= -1.0) {
      angle = PI_M;
   } else {
      angle = acos(cosine);
   }
   double deltaIdeal         = angle - angleParameters[0];
   double deltaIdeal2        = deltaIdeal*deltaIdeal;

  *dEdR                          = angleParameters[1]*deltaIdeal;
  *energyTerm                    = 0.5*angleParameters[1]*deltaIdeal2;

}

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

   Calculate Angle Bond ixn

   @param atomIndices      two bond indices
   @param atomCoordinates  atom coordinates
   @param parameters       parameters: parameters[0] = ideal bond length
                                       parameters[1] = bond k (includes factor of 2)
   @param forces           force array (forces added)
   @param totalEnergy      if not null, the energy will be added to this

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

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

    static const int LastAtomIndex      = 3;

   double deltaR[2][ReferenceForce::LastDeltaRIndex];

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

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

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

   double pVector[3];
   SimTKOpenMMUtilities::crossProductVector3(deltaR[0], deltaR[1], pVector);
   double rp = sqrt(DOT3(pVector, pVector));
   if (rp < 1.0e-06) {
      rp = 1.0e-06;
   }   
   double dot             = DOT3(deltaR[0], deltaR[1]);
   double cosine          = dot/sqrt((deltaR[0][ReferenceForce::R2Index]*deltaR[1][ReferenceForce::R2Index]));

   double dEdR;
   double energy;
   getPrefactorsGivenAngleCosine(cosine, parameters, &dEdR, &energy);

   double termA           =  dEdR/(deltaR[0][ReferenceForce::R2Index]*rp);
   double termC           = -dEdR/(deltaR[1][ReferenceForce::R2Index]*rp);

   double deltaCrossP[LastAtomIndex][3];
   SimTKOpenMMUtilities::crossProductVector3(deltaR[0], pVector, deltaCrossP[0]);
   SimTKOpenMMUtilities::crossProductVector3(deltaR[1], pVector, deltaCrossP[2]);

   for (int ii = 0; ii < 3; ii++) {
      deltaCrossP[0][ii] *= termA;
      deltaCrossP[2][ii] *= termC;
      deltaCrossP[1][ii]  = -(deltaCrossP[0][ii] + deltaCrossP[2][ii]);
   }   

   // accumulate forces
 
   for (int jj = 0; jj < LastAtomIndex; jj++) {
      for (int ii = 0; ii < 3; ii++) {
         forces[atomIndices[jj]][ii] += deltaCrossP[jj][ii];
      }   
   }   

   // accumulate energies

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