ReferenceRbDihedralBond.cpp

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

#include "../SimTKUtilities/SimTKOpenMMCommon.h"
#include "../SimTKUtilities/SimTKOpenMMLog.h"
#include "../SimTKUtilities/SimTKOpenMMUtilities.h"
#include "ReferenceRbDihedralBond.h"
#include "ReferenceForce.h"

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

   ReferenceRbDihedralBond constructor

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

ReferenceRbDihedralBond::ReferenceRbDihedralBond( ){

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

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

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

}

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

   ReferenceRbDihedralBond destructor

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

ReferenceRbDihedralBond::~ReferenceRbDihedralBond( ){

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

   // 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)
   @param energiesByBond   energies by bond: energiesByBond[bondIndex]
   @param energiesByAtom   energies by atom: energiesByAtom[atomIndex]

   @return ReferenceForce::DefaultReturn

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

int ReferenceRbDihedralBond::calculateBondIxn( int* atomIndices,
                                               RealOpenMM** atomCoordinates,
                                               RealOpenMM* parameters,
                                               RealOpenMM** forces,
                                               RealOpenMM* energiesByBond,
                                               RealOpenMM* energiesByAtom ) const {

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

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

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

   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;

   // debug flag

   static const int debug              = 0;

   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];
   ReferenceForce::getDeltaR( atomCoordinates[atomBIndex], atomCoordinates[atomAIndex], deltaR[0] );  
   ReferenceForce::getDeltaR( atomCoordinates[atomBIndex], atomCoordinates[atomCIndex], deltaR[1] );  
   ReferenceForce::getDeltaR( atomCoordinates[atomDIndex], atomCoordinates[atomCIndex], deltaR[2] );  

   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;
   RealOpenMM dihederalAngle = getDihedralAngleBetweenThreeVectors( deltaR[0], deltaR[1], deltaR[2],
                                                                    crossProduct, &cosPhi, deltaR[0], 
                                                                    &signOfAngle, hasREntry );

   // Gromacs: use polymer convention

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

   // Ryckaert-Bellemans:

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

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

   dEdAngle *= SIN( dihederalAngle );

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

   RealOpenMM 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];

      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

   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

   updateEnergy( energy, energiesByBond, LastAtomIndex, atomIndices, energiesByAtom );

   // debug 

   if( debug ){
      static bool printHeader = false;
      std::stringstream message;
      message << methodName;
      message << std::endl;
      if( !printHeader  ){  
         printHeader = true;
         message << std::endl;
         message << methodName.c_str() << " a0 k [c q p s] r1 r2  angle dt rp p[] dot cosine angle dEdR*r F[]" << std::endl;
      }   

      message << std::endl;
      for( int ii = 0; ii < 4; ii++ ){
         message << " Atm " << atomIndices[ii] << " [" << atomCoordinates[atomIndices[ii]][0] << " ";
         message <<            atomCoordinates[atomIndices[ii]][1] << "  " << atomCoordinates[atomIndices[ii]][2] << "] ";
      }
      message << std::endl << " Delta:";
      for( int ii = 0; ii < (LastAtomIndex - 1); ii++ ){
         message << " [";
         for( int jj = 0; jj < ReferenceForce::LastDeltaRIndex; jj++ ){
            message << deltaR[ii][jj] << " ";
         }
         message << "]";
      }
      message << std::endl;

      message << std::endl << " Cross:";
      for( int ii = 0; ii < 2; ii++ ){
         message << " [";
         for( int jj = 0; jj < 3; jj++ ){
            message << crossProduct[ii][jj] << " ";
         }
         message << "]";
      }
      message << std::endl;

      message << " k="     << parameters[0];
      message << " a="     << parameters[1];
      message << " m="     << parameters[2];
      message << " ang="   << dihederalAngle;
      message << " dotD="  << cosPhi;
      message << " sign="  << signOfAngle;
      message << std::endl << "  ";

      message << " dEdAngle=" << dEdAngle;
      message << " E=" << energy << " force factors: [";
      for( int ii = 0; ii < 4; ii++ ){
         message << forceFactors[ii] << " ";
      }
      message << "] F=compute force; f=cumulative force";

      message << std::endl << "  ";
      for( int ii = 0; ii < LastAtomIndex; ii++ ){
         message << " F" << (ii+1) << "[";
         SimTKOpenMMUtilities::formatRealStringStream( message, internalF[ii], threeI );
         message << "]";
      }   
      message << std::endl << "  ";

      for( int ii = 0; ii < LastAtomIndex; ii++ ){
         message << " f" << (ii+1) << "[";
         SimTKOpenMMUtilities::formatRealStringStream( message, forces[atomIndices[ii]], threeI );
         message << "]";
      }

      SimTKOpenMMLog::printMessage( message );
   }   

   if( debug ){
      std::stringstream message;
      message << methodName << " DONE";
      message << std::endl;
      SimTKOpenMMLog::printMessage( message );
   }

   return ReferenceForce::DefaultReturn;
}