RPMDIntegrator.h

#ifndef OPENMM_RPMDINTEGRATOR_H_
#define OPENMM_RPMDINTEGRATOR_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 "openmm/Integrator.h"
#include "openmm/Kernel.h"
#include "openmm/State.h"
#include "openmm/Vec3.h"
#include "openmm/internal/windowsExportRpmd.h"
#include <map>

namespace OpenMM {

class OPENMM_EXPORT_RPMD RPMDIntegrator : public Integrator {
public:
    RPMDIntegrator(int numCopies, double temperature, double frictionCoeff, double stepSize);
    RPMDIntegrator(int numCopies, double temperature, double frictionCoeff, double stepSize, const std::map<int, int>& contractions);
    int getNumCopies() const {
        return numCopies;
    }
    double getTemperature() const {
        return temperature;
    }
    void setTemperature(double temp) {
        temperature = temp;
    }
    double getFriction() const {
        return friction;
    }
    void setFriction(double coeff) {
        friction = coeff;
    }
    bool getApplyThermostat() const {
        return applyThermostat;
    }
    void setApplyThermostat(bool apply) {
        applyThermostat = apply;
    }
    int getRandomNumberSeed() const {
        return randomNumberSeed;
    }
    void setRandomNumberSeed(int seed) {
        randomNumberSeed = seed;
    }
    const std::map<int, int>& getContractions() const {
        return contractions;
    }
    void setPositions(int copy, const std::vector<Vec3>& positions);
    void setVelocities(int copy, const std::vector<Vec3>& velocities);
    State getState(int copy, int types, bool enforcePeriodicBox=false, int groups=0xFFFFFFFF);
    double getTotalEnergy();
    void step(int steps);
protected:
    void initialize(ContextImpl& context);
    void cleanup();
    void stateChanged(State::DataType changed);
    std::vector<std::string> getKernelNames();
    double computeKineticEnergy();
private:
    double temperature, friction;
    int numCopies, randomNumberSeed;
    bool applyThermostat;
    std::map<int, int> contractions;
    bool forcesAreValid, hasSetPosition, hasSetVelocity, isFirstStep;
    Kernel kernel;
};

} // namespace OpenMM

#endif /*OPENMM_RPMDINTEGRATOR_H_*/