ReferenceBondForce.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
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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:
 *
 * 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
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#include <string.h>
#include <sstream>

#include "../SimTKUtilities/SimTKOpenMMCommon.h"
#include "../SimTKUtilities/SimTKOpenMMLog.h"
#include "../SimTKUtilities/SimTKOpenMMUtilities.h"
#include "ReferenceBondForce.h"

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

   ReferenceBondForce constructor

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

ReferenceBondForce::ReferenceBondForce( ){

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

   // static const char* methodName = "\nReferenceBondForce::ReferenceBondForce";

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

}

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

   ReferenceBondForce destructor

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

ReferenceBondForce::~ReferenceBondForce( ){

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

   // static const char* methodName = "\nReferenceBondForce::~ReferenceBondForce";

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

}

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

   Calculate forces/energy for bonds

   @param numberOfBonds    number of bonds
   @param atomIndices      indices of atoms participating in bond ixn: atomIndices[bondIndex][indices]
   @param atomCoordinates  atom coordinates: atomCoordinates[atomIndex][3]
   @param parameters       parameters: parameters[bondIndex][*]; contents of array 
                           depend on ixn
   @param forces           force array (forces added to current values): forces[atomIndex][3]
   @param energiesByBond   energies by bond: energiesByBond[bondIndex]
   @param energiesByAtom   energies by atom: energiesByAtom[atomIndex]
   @param totalEnergy      totalEnergy: sum over { energies[atomIndex] }
   @param ReferenceBondIxn ixn to be calculated

   @return  ReferenceForce::DefaultReturn

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

int ReferenceBondForce::calculateForce( int numberOfBonds, int** atomIndices,
                                        RealOpenMM** atomCoordinates,
                                        RealOpenMM** parameters,
                                        RealOpenMM** forces, 
                                        RealOpenMM* energiesByBond, 
                                        RealOpenMM* energiesByAtom, 
                                        RealOpenMM *totalEnergy, 
                                        ReferenceBondIxn& referenceBondIxn ){


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

   static const char* methodName = "\nReferenceBondForce::calculateForce";

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

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

      // calculate bond ixn

      referenceBondIxn.calculateBondIxn( atomIndices[ii], atomCoordinates, parameters[ii], 
                                         forces, (energiesByBond == NULL ? NULL : energiesByBond + ii), energiesByAtom ); 

      if( energiesByBond != NULL ){
         *totalEnergy += energiesByBond[ii];
      }
   }

   return ReferenceForce::DefaultReturn;
}