NMLIntegrator.h

#ifndef OPENMM_NMLIntegrator_H_
#define OPENMM_NMLIntegrator_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) 2009 Stanford University and the Authors.           *
 * Authors: Chris Sweet                                                       *
 * Contributors: Christopher Bruns                                            *
 *                                                                            *
 * 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/internal/windowsExport.h"
#include "EigenvectorInfo.h"

namespace OpenMM {

/**
 * This is an Integrator which simulates a System using Langevin dynamics.
 */

class OPENMM_EXPORT NMLIntegrator : public Integrator {
public:
    /**
     * Create a NMLIntegrator.
     *
     * @param temperature    the temperature of the heat bath (in Kelvin)
     * @param frictionCoeff  the friction coefficient which couples the system to the heat bath
     * @param stepSize       the step size with which to integrator the system (in picoseconds)
     */
    NMLIntegrator(double temperature, double frictionCoeff, double stepSize, ProtoMol::EigenvectorInfo* projectionVectorInfo );
    /**
     * Get the temperature of the heat bath (in Kelvin).
     */
    double getTemperature() const {
        return temperature;
    }
    /**
     * Set the temperature of the heat bath (in Kelvin).
     */
    void setTemperature(double temp) {
        temperature = temp;
    }
    /**
     * Get the friction coefficient which determines how strongly the system is coupled to
     * the heat bath.
     */
    double getFriction() const {
        return friction;
    }
    /**
     * Set the friction coefficient which determines how strongly the system is coupled to
     * the heat bath.
     */
    void setFriction(double coeff) {
        friction = coeff;
    }


	  void setProjectionVectorInfo( ProtoMol::EigenvectorInfo* inVectorInfo ){
		  mProjectionVectorInfo = inVectorInfo;
	  }

	  ProtoMol::EigenvectorInfo* getProjectionVectorInfo() const{
		  return mProjectionVectorInfo;
	  }

    unsigned int getNumProjectionVectors() const{
      //return mProjectionVectorInfo->myNumEigenvectors;
      return mProjectionVectorInfo->myNumUsedEigenvectors;
    }

    double getMinimumLimit() const{
      return mProjectionVectorInfo->myMinimumLimit *  4.184; //Kcal->KJ
    }

    bool getProjVecChanged() const{      
      return mProjectionVectorInfo->myEigVecChanged;
    }

    double* getProjectionVectors() const{      
      return mProjectionVectorInfo->myEigenvectors;
    }

    void setProjVecChanged(bool inChanged){		  
      mProjectionVectorInfo->myEigVecChanged = inChanged;
    }

    double getMaxEigenvalue() const{
        //return max eigenvalue (f^2) in 1/ps from 1/charmm
      return mProjectionVectorInfo->myMaxEigenvalue * 
        (1000.0 / 48.88821290839616) * (1000.0 / 48.88821290839616) //(1/charmm to 1/ps)^2
        * 100.0; //(Angstron to nm [inverse])^2
    }

    /**
     * Advance a simulation through time by taking a series of time steps.
     *
     * @param steps   the number of time steps to take
     */
    void step(int steps);
    
    //Minimizer
    void minimize(int maxsteps);
    
protected:
    /**
     * This will be called by the OpenMMContext when it is created.  It informs the Integrator
     * of what context it will be integrating, and gives it a chance to do any necessary initialization.
     * It will also get called again if the application calls reinitialize() on the OpenMMContext.
     */
    void initialize(ContextImpl& context);
    /**
     * Get the names of all Kernels used by this Integrator.
     */
    std::vector<std::string> getKernelNames();
private:
	  ProtoMol::EigenvectorInfo* mProjectionVectorInfo;

    double temperature, friction;
    ContextImpl* context;
    Kernel kernel;
};

} // namespace OpenMM

#endif /*OPENMM_NMLIntegrator_H_*/