NonbondedForce.cpp

/* -------------------------------------------------------------------------- *
 *                                   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.               *
 *                                                                            *
 * Portions copyright (c) 2008 Stanford University and the Authors.           *
 * Authors: Peter Eastman                                                     *
 * Contributors:                                                              *
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#include "Force.h"
#include "OpenMMException.h"
#include "NonbondedForce.h"
#include "internal/NonbondedForceImpl.h"

using namespace OpenMM;

NonbondedForce::NonbondedForce(int numAtoms, int numNonbonded14) : atoms(numAtoms), nb14s(numNonbonded14),
        nonbondedMethod(NoCutoff), cutoffDistance(1.0) {
    periodicBoxVectors[0] = Vec3(2, 0, 0);
    periodicBoxVectors[1] = Vec3(0, 2, 0);
    periodicBoxVectors[2] = Vec3(0, 0, 2);
}

NonbondedForce::NonbondedMethod NonbondedForce::getNonbondedMethod() const {
    return nonbondedMethod;
}

void NonbondedForce::setNonbondedMethod(NonbondedMethod method) {
    nonbondedMethod = method;
}

double NonbondedForce::getCutoffDistance() const {
    return cutoffDistance;
}

void NonbondedForce::setCutoffDistance(double distance) {
    cutoffDistance = distance;
}

void NonbondedForce::getPeriodicBoxVectors(Vec3& a, Vec3& b, Vec3& c) const {
    a = periodicBoxVectors[0];
    b = periodicBoxVectors[1];
    c = periodicBoxVectors[2];
}

void NonbondedForce::setPeriodicBoxVectors(Vec3 a, Vec3 b, Vec3 c) {
    if (a[1] != 0.0 || a[2] != 0.0)
        throw OpenMMException("First periodic box vector must be parallel to x.");
    if (b[0] != 0.0 || b[2] != 0.0)
        throw OpenMMException("Second periodic box vector must be parallel to y.");
    if (c[0] != 0.0 || c[1] != 0.0)
        throw OpenMMException("Third periodic box vector must be parallel to z.");
    periodicBoxVectors[0] = a;
    periodicBoxVectors[1] = b;
    periodicBoxVectors[2] = c;
}

void NonbondedForce::getAtomParameters(int index, double& charge, double& radius, double& depth) const {
    charge = atoms[index].charge;
    radius = atoms[index].radius;
    depth = atoms[index].depth;
}

void NonbondedForce::setAtomParameters(int index, double charge, double radius, double depth) {
    atoms[index].charge = charge;
    atoms[index].radius = radius;
    atoms[index].depth = depth;
}

void NonbondedForce::getNonbonded14Parameters(int index, int& atom1, int& atom2, double& charge, double& radius, double& depth) const {
    atom1 = nb14s[index].atom1;
    atom2 = nb14s[index].atom2;
    charge = nb14s[index].charge;
    radius = nb14s[index].radius;
    depth = nb14s[index].depth;
}

void NonbondedForce::setNonbonded14Parameters(int index, int atom1, int atom2, double charge, double radius, double depth) {
    nb14s[index].atom1 = atom1;
    nb14s[index].atom2 = atom2;
    nb14s[index].charge = charge;
    nb14s[index].radius = radius;
    nb14s[index].depth = depth;
}

ForceImpl* NonbondedForce::createImpl() {
    return new NonbondedForceImpl(*this);
}