GBVIForce.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) 2008-2009 Stanford University and the Authors.      *
 * Authors: Peter Eastman                                                     *
 * Contributors:                                                              *
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#include "openmm/Force.h"
#include "openmm/OpenMMException.h"
#include "openmm/GBVIForce.h"
#include "openmm/internal/AssertionUtilities.h"
#include "openmm/internal/GBVIForceImpl.h"
#include <sstream>

using namespace OpenMM;

GBVIForce::GBVIForce() : nonbondedMethod(NoCutoff), cutoffDistance(1.0), solventDielectric(78.3), soluteDielectric(1.0),
                         scalingMethod(QuinticSpline), quinticLowerLimitFactor(0.8), quinticUpperBornRadiusLimit(5.0) {
}

int GBVIForce::addParticle(double charge, double radius, double gamma) {
    particles.push_back(ParticleInfo(charge, radius, gamma));
    return particles.size()-1;
}

void GBVIForce::getParticleParameters(int index, double& charge, double& radius, double& gamma) const {
    ASSERT_VALID_INDEX(index, particles);
    charge = particles[index].charge;
    radius = particles[index].radius;
    gamma  = particles[index].gamma;
}

void GBVIForce::setParticleParameters(int index, double charge, double radius, double gamma) {
    ASSERT_VALID_INDEX(index, particles);
    particles[index].charge = charge;
    particles[index].radius = radius;
    particles[index].gamma  = gamma;
}

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

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

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

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

GBVIForce::BornRadiusScalingMethod GBVIForce::getBornRadiusScalingMethod( void ) const {
    return scalingMethod;
}

void GBVIForce::setBornRadiusScalingMethod(BornRadiusScalingMethod method) {
    scalingMethod = method;
}

double GBVIForce::getQuinticLowerLimitFactor( void ) const {
    return quinticLowerLimitFactor;
}

void GBVIForce::setQuinticLowerLimitFactor(double inputQuinticLowerLimitFactor ){
    quinticLowerLimitFactor = inputQuinticLowerLimitFactor;
}

double GBVIForce::getQuinticUpperBornRadiusLimit( void ) const {
    return quinticUpperBornRadiusLimit;
}

void GBVIForce::setQuinticUpperBornRadiusLimit(double inputQuinticUpperBornRadiusLimit){
    quinticUpperBornRadiusLimit = inputQuinticUpperBornRadiusLimit;
}

int GBVIForce::addBond(int particle1, int particle2, double bondLength) {
    bonds.push_back(BondInfo(particle1, particle2, bondLength));
    return bonds.size()-1;
}

void GBVIForce::setBondParameters( int index, int particle1, int particle2, double bondLength) {
    ASSERT_VALID_INDEX(index, bonds);
    bonds[index].particle1  = particle1;
    bonds[index].particle2  = particle2;
    bonds[index].bondLength = bondLength;
}

int GBVIForce::getNumBonds( void ) const {
   return (int) bonds.size();
}

void GBVIForce::getBondParameters(int index, int& bondIndex1, int& bondIndex2, double& bondLength) const {
    ASSERT_VALID_INDEX(index, bonds);
    bondIndex1 = bonds[index].particle1;
    bondIndex2 = bonds[index].particle2;
    bondLength = bonds[index].bondLength;
}

ForceImpl* GBVIForce::createImpl() {
    return new GBVIForceImpl(*this);
}