Instrumentation/HarmonicTrimers.hpp

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/**
 * @file
 * Defines the OpenMPCD::CUDA::MPCFluid::Instrumentation::HarmonicTrimers class.
 */
 
#ifndef OPENMPCD_CUDA_MPCFLUID_INSTRUMENTATION_HARMONICTRIMERS_HPP
#define OPENMPCD_CUDA_MPCFLUID_INSTRUMENTATION_HARMONICTRIMERS_HPP
 
#include <OpenMPCD/CUDA/MPCFluid/HarmonicTrimers.hpp>
#include <OpenMPCD/CUDA/MPCFluid/Instrumentation/Base.hpp>
#include <OpenMPCD/CUDA/Simulation.hpp>
#include <OpenMPCD/Graph.hpp>
#include <OpenMPCD/Histogram.hpp>
 
#include <vector>
 
namespace OpenMPCD
{
namespace CUDA
{
namespace MPCFluid
{
namespace Instrumentation
{
/**
 * Instrumentation for Harmonic Trimer fluids.
 */
class HarmonicTrimers : public Base
{
    public:
        /**
         * The constructor.
         * @param[in] sim       The simulation instance.
         * @param[in] devMemMgr The Device memory manager.
         * @param[in] mpcFluid_ The MPC fluid to measure.
         */
        HarmonicTrimers(
            const Simulation* const sim, DeviceMemoryManager* const devMemMgr,
            const MPCFluid::HarmonicTrimers* const mpcFluid_);
 
        /**
         * The destructor.
         */
        virtual ~HarmonicTrimers()
        {
        }
 
    protected:
        /**
         * Performs measurements.
         */
        virtual void measureSpecific();
 
        /**
         * Saves the data to the given run directory.
         * @param[in] rundir The path to the run directory.
         */
        virtual void saveSpecific(const std::string& rundir) const;
 
    private:
        /**
         * Returns the number of trimers.
         */
        unsigned int getTrimerCount() const
        {
            return mpcFluid->getParticleCount()/3;
        }
 
        /**
         * Returns the center of mass coordinates for the trimer with the given ID.
         * @param[in] trimerID The ID of the trimer.
         * @throw OutOfBoundsException If OPENMPCD_DEBUG is defined, throws if trimerID>=getTrimerCount()
         */
        const Vector3D<MPCParticlePositionType> getTrimerCenterOfMass(const unsigned int trimerID) const;
 
    private:
        const Simulation* const simulation; ///< The simulation instance.
        const MPCFluid::HarmonicTrimers* const mpcFluid; ///< The fluid to measure.
 
        Histogram bond1LengthHistogram; ///< Histogram for the bond lengths between particles 1 and 2.
        Histogram bond2LengthHistogram; ///< Histogram for the bond lengths between particles 2 and 3.
 
        Histogram bond1LengthSquaredHistogram; ///< Histogram for the squares of the bond length between particles 1 and 2.
        Histogram bond2LengthSquaredHistogram; ///< Histogram for the squares of the bond length between particles 2 and 3.
 
        Histogram bond1XXHistogram; ///< Histogram for the squares of the x components of the bond 1.
        Histogram bond2XXHistogram; ///< Histogram for the squares of the x components of the bond 2.
 
        Histogram bond1YYHistogram; ///< Histogram for the squares of the y components of the bond 1.
        Histogram bond2YYHistogram; ///< Histogram for the squares of the y components of the bond 2.
 
        Histogram bond1ZZHistogram; ///< Histogram for the squares of the z components of the bond 1.
        Histogram bond2ZZHistogram; ///< Histogram for the squares of the z components of the bond 2.
 
        Histogram bond1XYHistogram; ///< Histogram for the product of the x and y components of the first bond.
        Histogram bond2XYHistogram; ///< Histogram for the product of the x and y components of the second bond.
 
        Histogram bond1XYAngleWithFlowDirectionHistogram; /**< Histogram for the angle between the 1-2 bond
                                                               vector's projection to the xy plane and the flow
                                                               direction.*/
        Histogram bond2XYAngleWithFlowDirectionHistogram; /**< Histogram for the angle between the 2-3 bond
                                                               vector's projection to the xy plane and the flow
                                                               direction.*/
 
 
        FP selfDiffusionCoefficientMeasurementTime;
            ///< The time each measurement of the self-diffusion coefficient \f$D\f$ takes.
        Graph selfDiffusionCoefficients;
            ///< Holds the measured self-diffusion coefficients \f$D\f$ and the time they ware taken.
        std::vector<Vector3D<MPCParticlePositionType> > trimerCenterOfMassesSnapshot;
            ///< Holds the center-of-mass coordinates of the trimers at a given point in time.
        FP trimerCenterOfMassesSnapshotTime; ///< The simulation time at which trimerCenterOfMassesSnapshot was taken.
}; //class HarmonicTrimers
} //namespace Instrumentation
} //namespace MPCFluid
} //namespace CUDA
} //namespace OpenMPCD
 
#endif