ReferenceBondForce.cpp

/* Portions copyright (c) 2006-2016 Stanford University and Simbios.
 * Contributors: Pande Group
 *
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#include <string.h>
#include <sstream>

#include "SimTKOpenMMUtilities.h"
#include "ReferenceBondForce.h"

using std::vector;
using namespace OpenMM;

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

   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 totalEnergy      if not null, the energy will be added to this
   @param ReferenceBondIxn ixn to be calculated

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

void ReferenceBondForce::calculateForce(int numberOfBonds, int** atomIndices,
                                        vector<RealVec>& atomCoordinates,
                                        RealOpenMM** parameters,
                                        vector<RealVec>& forces, 
                                        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, totalEnergy, NULL);
   }
}