/* -------------------------------------------------------------------------- *
 *                                   OpenMM                                   *
 * -------------------------------------------------------------------------- *
 * This is part of the OpenMM molecular simulation toolkit originating from   *
 * Simbios, the NIH National Center for Physics-Based Simulation of           *
 * Biological Structures at Stanford, funded under the NIH Roadmap for        *
 * Medical Research, grant U54 GM072970. See https://simtk.org.               *
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 * Portions copyright (c) 2006-2025 Stanford University and the Authors.      *
 * Authors: Pande Group, Evan Pretti                                          *
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#include "SimTKOpenMMUtilities.h"
#include "ReferenceConstantPotential14.h"
#include "ReferenceForce.h"

using std::vector;
using namespace OpenMM;

ReferenceConstantPotential14::ReferenceConstantPotential14() : periodic(false) {
}

ReferenceConstantPotential14::~ReferenceConstantPotential14() {
}

void ReferenceConstantPotential14::setPeriodic(OpenMM::Vec3* vectors) {
    periodic = true;
    periodicBoxVectors[0] = vectors[0];
    periodicBoxVectors[1] = vectors[1];
    periodicBoxVectors[2] = vectors[2];
}

void ReferenceConstantPotential14::calculateBondIxn(
    vector<int>& atomIndices, vector<Vec3>& atomCoordinates,
    vector<double>& parameters, vector<Vec3>& forces,
    double* totalEnergy, double* energyParamDerivs
) {
    double deltaR[ReferenceForce::LastDeltaRIndex];

    int atomAIndex = atomIndices[0];
    int atomBIndex = atomIndices[1];
    if (periodic) {
        ReferenceForce::getDeltaRPeriodic(atomCoordinates[atomBIndex], atomCoordinates[atomAIndex], periodicBoxVectors, deltaR);
    }
    else {
        ReferenceForce::getDeltaR(atomCoordinates[atomBIndex], atomCoordinates[atomAIndex], deltaR);
    }

    double inverseR = 1.0 / deltaR[ReferenceForce::RIndex];
    double energy = ONE_4PI_EPS0 * parameters[0] * inverseR;
    double dEdR = energy * inverseR * inverseR;

    for (int ii = 0; ii < 3; ii++) {
        double force = dEdR * deltaR[ii];
        forces[atomAIndex][ii] += force;
        forces[atomBIndex][ii] -= force;
    }

    if (totalEnergy != NULL) {
        *totalEnergy += energy;
    }
}
