ReferenceForce.cpp

/* Portions copyright (c) 2006-2013 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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 * 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
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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
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#include <cstring>
#include <sstream>

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

#include <cstdio>

using OpenMM::RealVec;

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

   ReferenceForce constructor

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

ReferenceForce::ReferenceForce( ){
}

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

   ReferenceForce destructor

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

ReferenceForce::~ReferenceForce( ){
}

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

   Given two coordinates on a periodic lattice, return the difference between them.

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

RealOpenMM ReferenceForce::periodicDifference(RealOpenMM val1, RealOpenMM val2, RealOpenMM period) {
    RealOpenMM diff = val1-val2;
    RealOpenMM base = (RealOpenMM) (floor(diff/period+0.5)*period);
    return diff-base;

}

void ReferenceForce::getDeltaR( const RealVec& atomCoordinatesI, const RealVec& atomCoordinatesJ,
                               RealOpenMM* deltaR ){
   deltaR[XIndex]    = atomCoordinatesJ[0] - atomCoordinatesI[0];
   deltaR[YIndex]    = atomCoordinatesJ[1] - atomCoordinatesI[1];
   deltaR[ZIndex]    = atomCoordinatesJ[2] - atomCoordinatesI[2];

   deltaR[R2Index]   = DOT3( deltaR, deltaR );
   deltaR[RIndex]    = (RealOpenMM) SQRT( deltaR[R2Index] );
}

void ReferenceForce::getDeltaRPeriodic( const RealVec& atomCoordinatesI, const RealVec& atomCoordinatesJ,
                               const RealOpenMM* boxSize, RealOpenMM* deltaR ){
   deltaR[XIndex]    = periodicDifference(atomCoordinatesJ[0], atomCoordinatesI[0], boxSize[0]);
   deltaR[YIndex]    = periodicDifference(atomCoordinatesJ[1], atomCoordinatesI[1], boxSize[1]);
   deltaR[ZIndex]    = periodicDifference(atomCoordinatesJ[2], atomCoordinatesI[2], boxSize[2]);

   deltaR[R2Index]   = DOT3( deltaR, deltaR );
   deltaR[RIndex]    = (RealOpenMM) SQRT( deltaR[R2Index] );
}

void ReferenceForce::getDeltaRPeriodic( const RealVec& atomCoordinatesI, const RealVec& atomCoordinatesJ,
                               const RealVec* boxVectors, RealOpenMM* deltaR ){
    RealVec diff = atomCoordinatesJ-atomCoordinatesI;
    diff -= boxVectors[2]*floor(diff[2]/boxVectors[2][2]+0.5);
    diff -= boxVectors[1]*floor(diff[1]/boxVectors[1][1]+0.5);
    diff -= boxVectors[0]*floor(diff[0]/boxVectors[0][0]+0.5);
    deltaR[XIndex] = diff[0];
    deltaR[YIndex] = diff[1];
    deltaR[ZIndex] = diff[2];
    deltaR[R2Index] = diff.dot(diff);
    deltaR[RIndex] = SQRT(deltaR[R2Index]);
}

double* ReferenceForce::getVariablePointer(Lepton::CompiledExpression& expression, const std::string& name) {
    if (expression.getVariables().find(name) == expression.getVariables().end())
        return NULL;
    return &expression.getVariableReference(name);
}

void ReferenceForce::setVariable(double* pointer, double value) {
    if (pointer != NULL)
        *pointer = value;
}