NonbondedForce.h

#ifndef OPENMM_NONBONDEDFORCE_H_
#define OPENMM_NONBONDEDFORCE_H_

/* -------------------------------------------------------------------------- *
 *                                   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) 2008-2014 Stanford University and the Authors.      *
 * Authors: Peter Eastman                                                     *
 * Contributors:                                                              *
 *                                                                            *
 * Permission is hereby granted, free of charge, to any person obtaining a    *
 * copy of this software and associated documentation files (the "Software"), *
 * to deal in the Software without restriction, including without limitation  *
 * the rights to use, copy, modify, merge, publish, distribute, sublicense,   *
 * and/or sell copies of the Software, and to 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 in *
 * all copies or substantial portions of the Software.                        *
 *                                                                            *
 * 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. IN NO EVENT SHALL    *
 * THE AUTHORS, CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM,    *
 * DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR      *
 * OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE  *
 * USE OR OTHER DEALINGS IN THE SOFTWARE.                                     *
 * -------------------------------------------------------------------------- */

#include "Context.h"
#include "Force.h"
#include <map>
#include <set>
#include <utility>
#include <vector>
#include "internal/windowsExport.h"

namespace OpenMM {

class OPENMM_EXPORT NonbondedForce : public Force {
public:
    enum NonbondedMethod {
        NoCutoff = 0,
        CutoffNonPeriodic = 1,
        CutoffPeriodic = 2,
        Ewald = 3,
        PME = 4
    };
    NonbondedForce();
    int getNumParticles() const {
        return particles.size();
    }
    int getNumExceptions() const {
        return exceptions.size();
    }
    NonbondedMethod getNonbondedMethod() const;
    void setNonbondedMethod(NonbondedMethod method);
    double getCutoffDistance() const;
    void setCutoffDistance(double distance);
    bool getUseSwitchingFunction() const;
    void setUseSwitchingFunction(bool use);
    double getSwitchingDistance() const;
    void setSwitchingDistance(double distance);
    double getReactionFieldDielectric() const;
    void setReactionFieldDielectric(double dielectric);
    double getEwaldErrorTolerance() const;
    void setEwaldErrorTolerance(double tol);
    void getPMEParameters(double& alpha, int& nx, int& ny, int& nz) const;
    void setPMEParameters(double alpha, int nx, int ny, int nz);
    int addParticle(double charge, double sigma, double epsilon);
    void getParticleParameters(int index, double& charge, double& sigma, double& epsilon) const;
    void setParticleParameters(int index, double charge, double sigma, double epsilon);
    int addException(int particle1, int particle2, double chargeProd, double sigma, double epsilon, bool replace = false);
    void getExceptionParameters(int index, int& particle1, int& particle2, double& chargeProd, double& sigma, double& epsilon) const;
    void setExceptionParameters(int index, int particle1, int particle2, double chargeProd, double sigma, double epsilon);
    void createExceptionsFromBonds(const std::vector<std::pair<int, int> >& bonds, double coulomb14Scale, double lj14Scale);
    bool getUseDispersionCorrection() const {
        return useDispersionCorrection;
    }
    void setUseDispersionCorrection(bool useCorrection) {
        useDispersionCorrection = useCorrection;
    }
    int getReciprocalSpaceForceGroup() const;
    void setReciprocalSpaceForceGroup(int group);
    void updateParametersInContext(Context& context);
protected:
    ForceImpl* createImpl() const;
private:
    class ParticleInfo;
    class ExceptionInfo;
    NonbondedMethod nonbondedMethod;
    double cutoffDistance, switchingDistance, rfDielectric, ewaldErrorTol, alpha;
    bool useSwitchingFunction, useDispersionCorrection;
    int recipForceGroup, nx, ny, nz;
    void addExclusionsToSet(const std::vector<std::set<int> >& bonded12, std::set<int>& exclusions, int baseParticle, int fromParticle, int currentLevel) const;
    std::vector<ParticleInfo> particles;
    std::vector<ExceptionInfo> exceptions;
    std::map<std::pair<int, int>, int> exceptionMap;
};

class NonbondedForce::ParticleInfo {
public:
    double charge, sigma, epsilon;
    ParticleInfo() {
        charge = sigma = epsilon = 0.0;
    }
    ParticleInfo(double charge, double sigma, double epsilon) :
        charge(charge), sigma(sigma), epsilon(epsilon) {
    }
};

class NonbondedForce::ExceptionInfo {
public:
    int particle1, particle2;
    double chargeProd, sigma, epsilon;
    ExceptionInfo() {
        particle1 = particle2 = -1;
        chargeProd = sigma = epsilon = 0.0;
    }
    ExceptionInfo(int particle1, int particle2, double chargeProd, double sigma, double epsilon) :
        particle1(particle1), particle2(particle2), chargeProd(chargeProd), sigma(sigma), epsilon(epsilon) {
    }
};

} // namespace OpenMM

#endif /*OPENMM_NONBONDEDFORCE_H_*/