AmoebaVdwForce.h

#ifndef OPENMM_AMOEBA_VDW_FORCE_H_
#define OPENMM_AMOEBA_VDW_FORCE_H_

/* -------------------------------------------------------------------------- *
 *                              OpenMMAmoeba                                  *
 * -------------------------------------------------------------------------- *
 * 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) 2008-2012 Stanford University and the Authors.      *
 * Authors: Mark Friedrichs, 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 "openmm/Force.h"
#include "internal/windowsExportAmoeba.h"
#include <vector>

namespace OpenMM {

class OPENMM_EXPORT_AMOEBA AmoebaVdwForce : public Force {
public:
    enum NonbondedMethod {
        NoCutoff = 0,
        CutoffPeriodic = 1,
    };

    AmoebaVdwForce();

    int getNumParticles() const {
        return parameters.size();
    }

    void setParticleParameters(int particleIndex, int parentIndex, double sigma, double epsilon, double reductionFactor);

    void getParticleParameters(int particleIndex, int& parentIndex, double& sigma, double& epsilon, double& reductionFactor) const;


    int addParticle(int parentIndex, double sigma, double epsilon, double reductionFactor);

    void setSigmaCombiningRule(const std::string& sigmaCombiningRule);

    const std::string& getSigmaCombiningRule(void) const;

    void setEpsilonCombiningRule(const std::string& epsilonCombiningRule);

    const std::string& getEpsilonCombiningRule(void) const;

    bool getUseDispersionCorrection() const {
        return useDispersionCorrection;
    }

    void setUseDispersionCorrection(bool useCorrection) {
        useDispersionCorrection = useCorrection;
    }

    void setParticleExclusions(int particleIndex, const std::vector<int>& exclusions);

    void getParticleExclusions(int particleIndex, std::vector<int>& exclusions) const;

    void setCutoff(double cutoff);

    double getCutoff() const;

    NonbondedMethod getNonbondedMethod() const;

    void setNonbondedMethod(NonbondedMethod method);
    void updateParametersInContext(Context& context);
    bool usesPeriodicBoundaryConditions() const {
        return nonbondedMethod == AmoebaVdwForce::CutoffPeriodic;
    }
protected:
    ForceImpl* createImpl() const;
private:

    class VdwInfo;
    NonbondedMethod nonbondedMethod;
    double cutoff;
    bool useDispersionCorrection;

    std::string sigmaCombiningRule;
    std::string epsilonCombiningRule;

    std::vector< std::vector<int> > exclusions;
    std::vector<VdwInfo> parameters;
    std::vector< std::vector< std::vector<double> > > sigEpsTable;
};

class AmoebaVdwForce::VdwInfo {
public:
    int parentIndex;
    double reductionFactor, sigma, epsilon, cutoff;
    VdwInfo() {
        parentIndex = -1;
        reductionFactor      = 0.0;
        sigma                = 1.0;
        epsilon              = 0.0;
    }
    VdwInfo(int parentIndex, double sigma, double epsilon, double reductionFactor) :
        parentIndex(parentIndex), sigma(sigma), epsilon(epsilon), reductionFactor(reductionFactor)  {
    }
};

} // namespace OpenMM

#endif /*OPENMM_AMOEBA_VDW_FORCE_H_*/