ReferenceAngleBondIxn.cpp

/* 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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 * without limitation the rights to use, copy, modify, merge, publish,
 * 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:
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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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 * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS
 * OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
 * MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT.
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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) {

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

   // static const char* methodName = "\nReferenceAngleBondIxn::ReferenceAngleBondIxn";

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

}

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

   ReferenceAngleBondIxn destructor

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

ReferenceAngleBondIxn::~ReferenceAngleBondIxn() {

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

   // static const char* methodName = "\nReferenceAngleBondIxn::~ReferenceAngleBondIxn";

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

}

void ReferenceAngleBondIxn::setPeriodic(OpenMM::RealVec* 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(RealOpenMM cosine, RealOpenMM* angleParameters,
                                                          RealOpenMM* dEdR, RealOpenMM* energyTerm) const {

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

   // static const std::string methodName = "\nReferenceAngleBondIxn::getPrefactorsGivenAngleCosine";

   static const RealOpenMM zero        = 0.0;
   static const RealOpenMM one         = 1.0;
   static const RealOpenMM half        = 0.5;

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

   RealOpenMM angle;
   if (cosine >= one) {
      angle = zero;
   } else if (cosine <= -one) {
      angle = PI_M;
   } else {
      angle = ACOS(cosine);
   }
   RealOpenMM deltaIdeal         = angle - angleParameters[0];
   RealOpenMM deltaIdeal2        = deltaIdeal*deltaIdeal;

  *dEdR                          = angleParameters[1]*deltaIdeal;
  *energyTerm                    = half*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(int* atomIndices,
                                             vector<RealVec>& atomCoordinates,
                                             RealOpenMM* parameters,
                                             vector<RealVec>& forces,
                                             RealOpenMM* totalEnergy) const {

   // constants -- reduce Visual Studio warnings regarding conversions between float & double

   static const RealOpenMM zero        =  0.0;
   static const RealOpenMM one         =  1.0;
   static const RealOpenMM two         =  2.0;
   static const RealOpenMM three       =  3.0;
   static const RealOpenMM oneM        = -1.0;

   static const int threeI             = 3;

   static const int LastAtomIndex      = 3;

   RealOpenMM 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]);  
   }

   RealOpenMM pVector[threeI];
   SimTKOpenMMUtilities::crossProductVector3(deltaR[0], deltaR[1], pVector);
   RealOpenMM rp              = DOT3(pVector, pVector);
   rp                         = SQRT(rp);
   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 dEdR;
   RealOpenMM energy;
   getPrefactorsGivenAngleCosine(cosine, parameters, &dEdR, &energy);

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

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

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

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

   // accumulate energies

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