System.h

#ifndef OPENMM_SYSTEM_H_
#define OPENMM_SYSTEM_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) 2008-2009 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 "Vec3.h"
#include <vector>
#include "internal/windowsExport.h"

namespace OpenMM {

class OPENMM_EXPORT Force;
class OPENMM_EXPORT VirtualSite;

class OPENMM_EXPORT System {
public:
    System();
    ~System();
    int getNumParticles() const {
        return masses.size();
    }
    int addParticle(double mass) {
        masses.push_back(mass);
        return masses.size()-1;
    }
    double getParticleMass(int index) const;
    void setParticleMass(int index, double mass);
    void setVirtualSite(int index, VirtualSite* virtualSite);
    bool isVirtualSite(int index) const {
        return (index < (int) virtualSites.size() && virtualSites[index] != NULL);
    }
    const VirtualSite& getVirtualSite(int index) const;
    int getNumConstraints() const {
        return constraints.size();
    }
    int addConstraint(int particle1, int particle2, double distance);
    void getConstraintParameters(int index, int& particle1, int& particle2, double& distance) const;
    void setConstraintParameters(int index, int particle1, int particle2, double distance);
    void removeConstraint(int index);
    int addForce(Force* force) {
        forces.push_back(force);
        return forces.size()-1;
    }
    int getNumForces() const {
        return forces.size();
    }
    const Force& getForce(int index) const;
    Force& getForce(int index);
    void removeForce(int index);
    void getDefaultPeriodicBoxVectors(Vec3& a, Vec3& b, Vec3& c) const;
    void setDefaultPeriodicBoxVectors(const Vec3& a, const Vec3& b, const Vec3& c);
    bool usesPeriodicBoundaryConditions();
private:
    class ConstraintInfo;
    Vec3 periodicBoxVectors[3];
    std::vector<double> masses;
    std::vector<ConstraintInfo> constraints;
    std::vector<Force*> forces;
    std::vector<VirtualSite*> virtualSites;
};

class System::ConstraintInfo {
public:
    int particle1, particle2;
    double distance;
    ConstraintInfo() {
        particle1 = particle2 = -1;
        distance = 0.0;
    }
    ConstraintInfo(int particle1, int particle2, double distance) :
        particle1(particle1), particle2(particle2), distance(distance) {
    }
};

} // namespace OpenMM

#endif /*OPENMM_SYSTEM_H_*/