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
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 *
 * 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
 * MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT.
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#include <cstring>
#include <sstream>

#include "SimTKOpenMMUtilities.h"
#include "ReferenceForce.h"

#include <cstdio>

using namespace OpenMM;

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

   ReferenceForce constructor

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

ReferenceForce::ReferenceForce() {
}

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

   ReferenceForce destructor

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

ReferenceForce::~ReferenceForce() {
}

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

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

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

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

}

void ReferenceForce::getDeltaR(const Vec3& atomCoordinatesI, const Vec3& atomCoordinatesJ,
                               double* 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]    = sqrt(deltaR[R2Index]);
}

Vec3 ReferenceForce::getDeltaR(const Vec3& atomCoordinatesI, const Vec3& atomCoordinatesJ) {
    return atomCoordinatesJ-atomCoordinatesI;
}

void ReferenceForce::getDeltaRPeriodic(const Vec3& atomCoordinatesI, const Vec3& atomCoordinatesJ,
                               const double* boxSize, double* 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]    = sqrt(deltaR[R2Index]);
}

void ReferenceForce::getDeltaRPeriodic(const Vec3& atomCoordinatesI, const Vec3& atomCoordinatesJ,
                               const Vec3* boxVectors, double* deltaR) {
    Vec3 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]);
}

Vec3 ReferenceForce::getDeltaRPeriodic(const Vec3& atomCoordinatesI, const Vec3& atomCoordinatesJ,
                               const Vec3* boxVectors) {
    Vec3 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);
    return diff;
}

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;
}