CustomIntegrator.h

#ifndef OPENMM_CUSTOMINTEGRATOR_H_
#define OPENMM_CUSTOMINTEGRATOR_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) 2011-2012 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 "Integrator.h"
#include "Vec3.h"
#include "openmm/Kernel.h"
#include "internal/windowsExport.h"
#include <string>
#include <vector>

namespace OpenMM {

class OPENMM_EXPORT CustomIntegrator : public Integrator {
public:
    enum ComputationType {
        ComputeGlobal = 0,
        ComputePerDof = 1,
        ComputeSum = 2,
        ConstrainPositions = 3,
        ConstrainVelocities = 4,
        UpdateContextState = 5
    };
    CustomIntegrator(double stepSize);
    int getNumGlobalVariables() const {
        return globalNames.size();
    }
    int getNumPerDofVariables() const {
        return perDofNames.size();
    }
    int getNumComputations() const {
        return computations.size();
    }
    int addGlobalVariable(const std::string& name, double initialValue);
    const std::string& getGlobalVariableName(int index) const;
    int addPerDofVariable(const std::string& name, double initialValue);
    const std::string& getPerDofVariableName(int index) const;
    double getGlobalVariable(int index) const;
    double getGlobalVariableByName(const std::string& name) const;
    void setGlobalVariable(int index, double value);
    void setGlobalVariableByName(const std::string& name, double value);
    void getPerDofVariable(int index, std::vector<Vec3>& values) const;
    void getPerDofVariableByName(const std::string& name, std::vector<Vec3>& values) const;
    void setPerDofVariable(int index, const std::vector<Vec3>& values);
    void setPerDofVariableByName(const std::string& name, const std::vector<Vec3>& values);
    int addComputeGlobal(const std::string& variable, const std::string& expression);
    int addComputePerDof(const std::string& variable, const std::string& expression);
    int addComputeSum(const std::string& variable, const std::string& expression);
    int addConstrainPositions();
    int addConstrainVelocities();
    int addUpdateContextState();
    void getComputationStep(int index, ComputationType& type, std::string& variable, std::string& expression) const;
    const std::string& getKineticEnergyExpression() const;
    void setKineticEnergyExpression(const std::string& expression);
    int getRandomNumberSeed() const {
        return randomNumberSeed;
    }
    void setRandomNumberSeed(int seed) {
        randomNumberSeed = seed;
    }
    void step(int steps);
protected:
    void initialize(ContextImpl& context);
    void cleanup();
    void stateChanged(State::DataType changed);
    std::vector<std::string> getKernelNames();
    double computeKineticEnergy();
private:
    class ComputationInfo;
    std::vector<std::string> globalNames;
    std::vector<std::string> perDofNames;
    mutable std::vector<double> globalValues;
    std::vector<std::vector<Vec3> > perDofValues;
    std::vector<ComputationInfo> computations;
    std::string kineticEnergy;
    mutable bool globalsAreCurrent;
    int randomNumberSeed;
    bool forcesAreValid;
    Kernel kernel;
};

class CustomIntegrator::ComputationInfo {
public:
    ComputationType type;
    std::string variable, expression;
    ComputationInfo() {
    }
    ComputationInfo(ComputationType type, const std::string& variable, const std::string& expression) :
        type(type), variable(variable), expression(expression) {
    }
};

} // namespace OpenMM

#endif /*OPENMM_CUSTOMINTEGRATOR_H_*/