CustomNonbondedForce.h

#ifndef OPENMM_CUSTOMNONBONDEDFORCE_H_
#define OPENMM_CUSTOMNONBONDEDFORCE_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 "TabulatedFunction.h"
#include "Force.h"
#include "Vec3.h"
#include <map>
#include <set>
#include <utility>
#include <vector>
#include "internal/windowsExport.h"

namespace OpenMM {

class OPENMM_EXPORT CustomNonbondedForce : public Force {
public:
    enum NonbondedMethod {
        NoCutoff = 0,
        CutoffNonPeriodic = 1,
        CutoffPeriodic = 2,
    };
    explicit CustomNonbondedForce(const std::string& energy);
    CustomNonbondedForce(const CustomNonbondedForce& rhs); // copy constructor
    ~CustomNonbondedForce();
    int getNumParticles() const {
        return particles.size();
    }
    int getNumExclusions() const {
        return exclusions.size();
    }
    int getNumPerParticleParameters() const {
        return parameters.size();
    }
    int getNumGlobalParameters() const {
        return globalParameters.size();
    }
    int getNumTabulatedFunctions() const {
        return functions.size();
    }
    int getNumFunctions() const {
        return functions.size();
    }
    int getNumInteractionGroups() const {
        return interactionGroups.size();
    }
    const std::string& getEnergyFunction() const;
    void setEnergyFunction(const std::string& energy);
    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);
    bool getUseLongRangeCorrection() const;
    void setUseLongRangeCorrection(bool use);
    int addPerParticleParameter(const std::string& name);
    const std::string& getPerParticleParameterName(int index) const;
    void setPerParticleParameterName(int index, const std::string& name);
    int addGlobalParameter(const std::string& name, double defaultValue);
    const std::string& getGlobalParameterName(int index) const;
    void setGlobalParameterName(int index, const std::string& name);
    double getGlobalParameterDefaultValue(int index) const;
    void setGlobalParameterDefaultValue(int index, double defaultValue);
    int addParticle(const std::vector<double>& parameters);
    void getParticleParameters(int index, std::vector<double>& parameters) const;
    void setParticleParameters(int index, const std::vector<double>& parameters);
    int addExclusion(int particle1, int particle2);
    void getExclusionParticles(int index, int& particle1, int& particle2) const;
    void setExclusionParticles(int index, int particle1, int particle2);
    void createExclusionsFromBonds(const std::vector<std::pair<int, int> >& bonds, int bondCutoff);
    int addTabulatedFunction(const std::string& name, TabulatedFunction* function);
    const TabulatedFunction& getTabulatedFunction(int index) const;
    TabulatedFunction& getTabulatedFunction(int index);
    const std::string& getTabulatedFunctionName(int index) const;
    int addFunction(const std::string& name, const std::vector<double>& values, double min, double max);
    void getFunctionParameters(int index, std::string& name, std::vector<double>& values, double& min, double& max) const;
    void setFunctionParameters(int index, const std::string& name, const std::vector<double>& values, double min, double max);
    int addInteractionGroup(const std::set<int>& set1, const std::set<int>& set2);
    void getInteractionGroupParameters(int index, std::set<int>& set1, std::set<int>& set2) const;
    void setInteractionGroupParameters(int index, const std::set<int>& set1, const std::set<int>& set2);
    void updateParametersInContext(Context& context);
    bool usesPeriodicBoundaryConditions() const {
        return nonbondedMethod == CustomNonbondedForce::CutoffPeriodic;
    }
protected:
    ForceImpl* createImpl() const;
private:
    // REMEMBER TO UPDATE THE COPY CONSTRUCTOR IF YOU ADD ANY NEW FIELDS !!
    class ParticleInfo;
    class PerParticleParameterInfo;
    class GlobalParameterInfo;
    class ExclusionInfo;
    class FunctionInfo;
    class InteractionGroupInfo;
    NonbondedMethod nonbondedMethod;
    double cutoffDistance, switchingDistance;
    bool useSwitchingFunction, useLongRangeCorrection;
    std::string energyExpression;
    std::vector<PerParticleParameterInfo> parameters;
    std::vector<GlobalParameterInfo> globalParameters;
    std::vector<ParticleInfo> particles;
    std::vector<ExclusionInfo> exclusions;
    std::vector<FunctionInfo> functions;
    std::vector<InteractionGroupInfo> interactionGroups;
};

class CustomNonbondedForce::ParticleInfo {
public:
    std::vector<double> parameters;
    ParticleInfo() {
    }
    ParticleInfo(const std::vector<double>& parameters) : parameters(parameters) {
    }
};

class CustomNonbondedForce::PerParticleParameterInfo {
public:
    std::string name;
    PerParticleParameterInfo() {
    }
    PerParticleParameterInfo(const std::string& name) : name(name) {
    }
};

class CustomNonbondedForce::GlobalParameterInfo {
public:
    std::string name;
    double defaultValue;
    GlobalParameterInfo() {
    }
    GlobalParameterInfo(const std::string& name, double defaultValue) : name(name), defaultValue(defaultValue) {
    }
};

class CustomNonbondedForce::ExclusionInfo {
public:
    int particle1, particle2;
    ExclusionInfo() {
        particle1 = particle2 = -1;
    }
    ExclusionInfo(int particle1, int particle2) :
        particle1(particle1), particle2(particle2) {
    }
};

class CustomNonbondedForce::FunctionInfo {
public:
    std::string name;
    TabulatedFunction* function;
    FunctionInfo() {
    }
    FunctionInfo(const std::string& name, TabulatedFunction* function) : name(name), function(function) {
    }
};

class CustomNonbondedForce::InteractionGroupInfo {
public:
    std::set<int> set1, set2;
    InteractionGroupInfo() {
    }
    InteractionGroupInfo(const std::set<int>& set1, const std::set<int>& set2) :
        set1(set1), set2(set2) {
    }
};

} // namespace OpenMM

#endif /*OPENMM_CUSTOMNONBONDEDFORCE_H_*/