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# RPMDIntegrator.h

    00001 #ifndef OPENMM_RPMDINTEGRATOR_H_
    00002 #define OPENMM_RPMDINTEGRATOR_H_
    00003
    00004 /* -------------------------------------------------------------------------- *
    00005  *                                   OpenMM                                   *
    00006  * -------------------------------------------------------------------------- *
    00007  * This is part of the OpenMM molecular simulation toolkit originating from   *
    00008  * Simbios, the NIH National Center for Physics-Based Simulation of           *
    00009  * Biological Structures at Stanford, funded under the NIH Roadmap for        *
    00010  * Medical Research, grant U54 GM072970. See https://simtk.org.               *
    00011  *                                                                            *
    00012  * Portions copyright (c) 2008-2014 Stanford University and the Authors.      *
    00013  * Authors: Peter Eastman                                                     *
    00014  * Contributors:                                                              *
    00015  *                                                                            *
    00016  * Permission is hereby granted, free of charge, to any person obtaining a    *
    00017  * copy of this software and associated documentation files (the "Software"), *
    00018  * to deal in the Software without restriction, including without limitation  *
    00019  * the rights to use, copy, modify, merge, publish, distribute, sublicense,   *
    00020  * and/or sell copies of the Software, and to permit persons to whom the      *
    00021  * Software is furnished to do so, subject to the following conditions:       *
    00022  *                                                                            *
    00023  * The above copyright notice and this permission notice shall be included in *
    00024  * all copies or substantial portions of the Software.                        *
    00025  *                                                                            *
    00026  * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR *
    00027  * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,   *
    00028  * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL    *
    00029  * THE AUTHORS, CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM,    *
    00030  * DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR      *
    00031  * OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE  *
    00032  * USE OR OTHER DEALINGS IN THE SOFTWARE.                                     *
    00033  * -------------------------------------------------------------------------- */
    00034
    00035 #include "openmm/Integrator.h"
    00036 #include "openmm/Kernel.h"
    00037 #include "openmm/State.h"
    00038 #include "openmm/Vec3.h"
    00039 #include "openmm/internal/windowsExportRpmd.h"
    00040 #include <map>
    00041
    00042 namespace OpenMM {
    00043
    00069 class OPENMM_EXPORT_RPMD RPMDIntegrator : public Integrator {
    00070 public:
    00079     RPMDIntegrator(int numCopies, double temperature, double frictionCoeff, double stepSize);
    00092     RPMDIntegrator(int numCopies, double temperature, double frictionCoeff, double stepSize, const std::map<int, int>& contractions);
    00096     int getNumCopies() const {
    00097         return numCopies;
    00098     }
    00104     double getTemperature() const {
    00105         return temperature;
    00106     }
    00112     void setTemperature(double temp) {
    00113         temperature = temp;
    00114     }
    00121     double getFriction() const {
    00122         return friction;
    00123     }
    00130     void setFriction(double coeff) {
    00131         friction = coeff;
    00132     }
    00136     bool getApplyThermostat() const {
    00137         return applyThermostat;
    00138     }
    00142     void setApplyThermostat(bool apply) {
    00143         applyThermostat = apply;
    00144     }
    00148     int getRandomNumberSeed() const {
    00149         return randomNumberSeed;
    00150     }
    00159     void setRandomNumberSeed(int seed) {
    00160         randomNumberSeed = seed;
    00161     }
    00168     const std::map<int, int>& getContractions() const {
    00169         return contractions;
    00170     }
    00177     void setPositions(int copy, const std::vector<Vec3>& positions);
    00184     void setVelocities(int copy, const std::vector<Vec3>& velocities);
    00197     State getState(int copy, int types, bool enforcePeriodicBox=false, int groups=0xFFFFFFFF);
    00202     double getTotalEnergy();
    00208     void step(int steps);
    00209 protected:
    00215     void initialize(ContextImpl& context);
    00220     void cleanup();
    00224     void stateChanged(State::DataType changed);
    00228     std::vector<std::string> getKernelNames();
    00232     double computeKineticEnergy();
    00233 private:
    00234     double temperature, friction;
    00235     int numCopies, randomNumberSeed;
    00236     bool applyThermostat;
    00237     std::map<int, int> contractions;
    00238     bool forcesAreValid, hasSetPosition, hasSetVelocity, isFirstStep;
    00239     Kernel kernel;
    00240 };
    00241
    00242 } // namespace OpenMM
    00243
    00244 #endif /*OPENMM_RPMDINTEGRATOR_H_*/