ReferenceRbDihedralBond.cpp 7.22 KB
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/* Portions copyright (c) 2006 Stanford University and Simbios.
 * Contributors: Pande Group
 *
 * Permission is hereby granted, free of charge, to any person obtaining
 * a copy of this software and associated documentation files (the
 * "Software"), to deal in the Software without restriction, including
 * 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:
 *
 * The above copyright notice and this permission notice shall be included
 * in all copies or substantial portions of the Software.
 *
 * 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.
 * IN NO EVENT SHALL THE AUTHORS, CONTRIBUTORS OR COPYRIGHT HOLDERS BE
 * LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION
 * OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION
 * WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */

#include <string.h>
#include <sstream>

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

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using std::vector;
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using namespace OpenMM;
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/**---------------------------------------------------------------------------------------

   ReferenceRbDihedralBond constructor

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

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ReferenceRbDihedralBond::ReferenceRbDihedralBond() {
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   // ---------------------------------------------------------------------------------------

   // static const char* methodName = "\nReferenceRbDihedralBond::ReferenceRbDihedralBond";

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

}

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

   ReferenceRbDihedralBond destructor

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

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ReferenceRbDihedralBond::~ReferenceRbDihedralBond() {
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   // ---------------------------------------------------------------------------------------

   // static const char* methodName = "\nReferenceRbDihedralBond::~ReferenceRbDihedralBond";

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

}

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

   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)
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   @param totalEnergy      if not null, the energy will be added to this
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   --------------------------------------------------------------------------------------- */

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void ReferenceRbDihedralBond::calculateBondIxn(int* atomIndices,
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                                               vector<RealVec>& atomCoordinates,
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                                               RealOpenMM* parameters,
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                                               vector<RealVec>& forces,
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                                               RealOpenMM* totalEnergy) const {
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   static const std::string methodName = "\nReferenceRbDihedralBond::calculateBondIxn";

   // 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;

   // number of parameters

   static const int numberOfParameters = 6;

   static const int LastAtomIndex      = 4;

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

   RealOpenMM 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];
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   ReferenceForce::getDeltaR(atomCoordinates[atomBIndex], atomCoordinates[atomAIndex], deltaR[0]);  
   ReferenceForce::getDeltaR(atomCoordinates[atomBIndex], atomCoordinates[atomCIndex], deltaR[1]);  
   ReferenceForce::getDeltaR(atomCoordinates[atomDIndex], atomCoordinates[atomCIndex], deltaR[2]);  
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   RealOpenMM cosPhi;
   RealOpenMM signOfAngle;
   int hasREntry             = 1;

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

   RealOpenMM* crossProduct[2];
   crossProduct[0]           = crossProductMemory;
   crossProduct[1]           = crossProductMemory + 3;
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   RealOpenMM dihederalAngle = getDihedralAngleBetweenThreeVectors(deltaR[0], deltaR[1], deltaR[2],
                                                                   crossProduct, &cosPhi, deltaR[0], 
                                                                   &signOfAngle, hasREntry);
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   // Gromacs: use polymer convention

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   if (dihederalAngle < zero) {
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      dihederalAngle += PI_M;
   } else {
      dihederalAngle -= PI_M;
   }
   cosPhi *= -one;

   // Ryckaert-Bellemans:

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

   RealOpenMM dEdAngle       = zero;
   RealOpenMM energy         = parameters[0];
   RealOpenMM cosFactor      = one;
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   for (int ii = 1; ii < numberOfParameters; ii++) {
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      dEdAngle  -= ((RealOpenMM) ii)*parameters[ii]*cosFactor;
      cosFactor *= cosPhi;
      energy    += cosFactor*parameters[ii];
   }

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

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   RealOpenMM normCross2         = DOT3(crossProduct[1], crossProduct[1]);
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              forceFactors[3]    = (dEdAngle*normBC)/normCross2;
  
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              forceFactors[1]    = DOT3(deltaR[0], deltaR[1]);
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              forceFactors[1]   /= deltaR[1][ReferenceForce::R2Index];

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

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   for (int ii = 0; ii < 3; ii++) {
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      internalF[0][ii]  = forceFactors[0]*crossProduct[0][ii];
      internalF[3][ii]  = forceFactors[3]*crossProduct[1][ii];

      RealOpenMM 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

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

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