ReferenceCustomAngleIxn.cpp

/* Portions copyright (c) 2010-2016 Stanford University and Simbios.
 * Contributors: Peter Eastman
 *
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 * permit persons to whom the Software is furnished to do so, subject
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#include <string.h>
#include <sstream>

#include "SimTKOpenMMUtilities.h"
#include "ReferenceCustomAngleIxn.h"
#include "ReferenceForce.h"

using namespace OpenMM;
using namespace std;

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

   ReferenceCustomAngleIxn constructor

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

ReferenceCustomAngleIxn::ReferenceCustomAngleIxn(const Lepton::CompiledExpression& energyExpression,
        const Lepton::CompiledExpression& forceExpression, const vector<string>& parameterNames, map<string, double> globalParameters) :
        energyExpression(energyExpression), forceExpression(forceExpression), usePeriodic(false) {
    
    energyTheta = ReferenceForce::getVariablePointer(this->energyExpression, "theta");
    forceTheta = ReferenceForce::getVariablePointer(this->forceExpression, "theta");
    numParameters = parameterNames.size();
    for (int i = 0; i < (int) numParameters; i++) {
        energyParams.push_back(ReferenceForce::getVariablePointer(this->energyExpression, parameterNames[i]));
        forceParams.push_back(ReferenceForce::getVariablePointer(this->forceExpression, parameterNames[i]));
    }
    for (map<string, double>::const_iterator iter = globalParameters.begin(); iter != globalParameters.end(); ++iter) {
        ReferenceForce::setVariable(ReferenceForce::getVariablePointer(this->energyExpression, iter->first), iter->second);
        ReferenceForce::setVariable(ReferenceForce::getVariablePointer(this->forceExpression, iter->first), iter->second);
    }
}

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

   ReferenceCustomAngleIxn destructor

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

ReferenceCustomAngleIxn::~ReferenceCustomAngleIxn() {
}

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

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

   Calculate Custom Angle Ixn

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

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

void ReferenceCustomAngleIxn::calculateBondIxn(int* atomIndices,
                                               vector<RealVec>& atomCoordinates,
                                               RealOpenMM* parameters,
                                               vector<RealVec>& forces,
                                               RealOpenMM* totalEnergy) const {

   static const std::string methodName = "\nReferenceCustomAngleIxn::calculateAngleIxn";

   static const RealOpenMM zero        = 0.0;
   static const RealOpenMM one         = 1.0;

   RealOpenMM deltaR[2][ReferenceForce::LastDeltaRIndex];
   for (int i = 0; i < numParameters; i++) {
       ReferenceForce::setVariable(energyParams[i], parameters[i]);
       ReferenceForce::setVariable(forceParams[i], parameters[i]);
   }

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

   // Compute the angle between the three 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]);
   }
   RealOpenMM pVector[3];
   SimTKOpenMMUtilities::crossProductVector3(deltaR[0], deltaR[1], pVector);
   RealOpenMM rp = SQRT(DOT3(pVector, pVector));
   if (rp < 1.0e-06)
      rp = (RealOpenMM) 1.0e-06;
   RealOpenMM dot = DOT3(deltaR[0], deltaR[1]);
   RealOpenMM cosine = dot/SQRT((deltaR[0][ReferenceForce::R2Index]*deltaR[1][ReferenceForce::R2Index]));
   RealOpenMM angle;
   if (cosine >= one)
      angle = zero;
   else if (cosine <= -one)
      angle = PI_M;
   else
      angle = ACOS(cosine);
   ReferenceForce::setVariable(energyTheta, angle);
   ReferenceForce::setVariable(forceTheta, angle);

   // Compute the force and energy, and apply them to the atoms.
   
   RealOpenMM energy = (RealOpenMM) energyExpression.evaluate();
   RealOpenMM dEdR = (RealOpenMM) forceExpression.evaluate();
   RealOpenMM termA =  dEdR/(deltaR[0][ReferenceForce::R2Index]*rp);
   RealOpenMM termC = -dEdR/(deltaR[1][ReferenceForce::R2Index]*rp);

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

   // accumulate energies

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