BaseCluster.h

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//Copyright (c) 2013-2020, The MercuryDPM Developers Team. All rights reserved.
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#ifndef BaseCluster_H
#define BaseCluster_H

#endif //BaseCluster_H

#include <Mercury3D.h>
#include "Species/LinearPlasticViscoelasticFrictionSpecies.h"


#ifdef MERCURY_USE_MPI
#include <mpi.h>
#include <MpiDataClass.h>
#include <MpiContainer.h>
#endif

#ifndef BaseCluster_h
#define BaseCluster_h
class BaseCluster : public Mercury3D
{
public:

/*
 * ----------------------------------------------------------------------
 *               FUNCTIONS: setters and getters
 * ----------------------------------------------------------------------
 */

    BaseCluster();

    ~BaseCluster() final;

    Vec3D getPosition() const;

    void setPosition(Vec3D p);

    Mdouble getCollisionTimeOverTimeStep() const;

    void setCollisionTimeOverTimeStep(Mdouble cTOTS);

    Mdouble getRadiusParticle() const;

    void setRadiusParticle(Mdouble rP);

    Mdouble getSizeDispersityParticle() const;

    void setSizeDispersityParticle(Mdouble sDP);

    int getNumberOfParticles() const;

    void setNumberOfParticles(int nP);

    void setRadiusCluster(Mdouble rCR);

    Mdouble getFinalMassFraction();

    unsigned int getClusterId() const;

    void setClusterId(unsigned int iC);

    Mdouble getVelocityDampingModulus() const;

    void setVelocityDampingModulus(Mdouble vDM);

    int getNumberOfInternalStructurePoints() const;

    void setNumberOfInternalStructurePoints(int gL);

    Mdouble getEnergyRatioTolerance() const;

    void setEnergyRatioTolerance(Mdouble eRT);

    LinearPlasticViscoelasticFrictionSpecies *getParticleSpecies() const;

    void setParticleSpecies(LinearPlasticViscoelasticFrictionSpecies *particleSpecies);

    Vec3D getVelocity();
    
    void setVelocity(Vec3D v);

    bool isCdatOutputOn() const;

    void doCdatOutput(bool iCOO);

    bool isOverlOutputOn() const;

    void doOverlOutput(bool iOOO);

    bool isAmatOutputOn() const;

    void doAmatOutput(bool iAOO);

    bool isIntStrucOutputOn() const;

    void doIntStrucOutput(bool iISOO);

    bool isVtkOutputOn() const;

    void doVtkOutput(bool iVOO);

    bool isRestartOutputOn() const;

    void doRestartOutput(bool isRestartOutputOn);

    bool isFStatOutputOn() const;

    void doFStatOutput(bool isfStatOutputOn);

    bool isEneOutputOn() const;

    void doEneOutput(bool isEneOutputOn);

    Mdouble getMeanClusterRadius();

    Mdouble getAverageOverlap();

/*
 * ----------------------------------------------------------------------
 *               FUNCTIONS: overridden mercury3D functions
 * ----------------------------------------------------------------------
 */


    void setupInitialConditions() override;

    void actionsAfterTimeStep() override;

    void actionsAfterSolve() override;

    void write(std::ostream& os, bool writeAllParticles ) const override;

    void read(std::istream& is, ReadOptions opt = ReadOptions::ReadAll) override;

    void actionsOnRestart() override;

    void printTime() const override;
    
private:
    /*
     * ----------------------------------------------------------------------
     *           FUNCTIONS: functions inside setupInitialConditions
     * ----------------------------------------------------------------------
     */

    void setRadii();

    void setSpecies();

    void setDomainLimits();

    void calculateTimeStep();

    void insertParticles();

    void makeCdatFile();

    void makeOverlFile();

    bool particleInsertionSuccessful(int n);



    /*
     * ----------------------------------------------------------------------
     *        FUNCTIONS: functions inside actionsAfterTimeStep
     * ----------------------------------------------------------------------
     */

    void makeDataAnalysis();

    void writeToCdatFile();

    void writeToOverlFile();

    void applyCentralForce();

    void increaseForce();

    void dampVelocities();

    void decreaseForce();

    void dampForce();

    void createAdjacencyMatrix();

    void makeAmatFile();

    void writeAmatFile();

    void computeInternalStructure();

    void makeGnuplotFile();

    void makeIntenalStructureFile();



    /*
     * ----------------------------------------------------------------------
     *       VARIABLES: accessed by the user with setters and getters
     * ----------------------------------------------------------------------
     */

    //POSITION
    //\brief Position where the cluster is inserted after creation.
    Vec3D position_;

    // TIME
    //\brief Ratio between collision time and time step: should be at least 50.
    Mdouble collisionTimeOverTimeStep_;
    // \brief Energy ratio threshold under wich the simulation can be considered static and so can be stopped.
    Mdouble energyRatioTolerance_;

    // PARTiCleS
    //\brief Radius basing on which all radii will be computed.
    Mdouble radiusParticle_;
    // \brief Bool that saves whether or not the user has set the radius of the single particle composing the cluster.
    bool setRadiusParticle_ = false;
    //\brief Size dispersity of particles: must be between >= than 1.
    Mdouble sizeDispersityParticle_;
    //\brief Total number of particles.
    int nParticles_;
    // \brief Bool that saves whether or not the user has set the number of particles
    bool setNumberOfParticles_ = false;

    // CLUSTER
    //\brief Total number of particles.
    unsigned int idCluster_;
    //\brief Desired radius of the cluster.
    Mdouble radiusCluster_;
    // \brief Bool that saves whether or not the user has set the cluster radius
    bool setRadiusCluster_ = false;
    //\brief Velocity of the cluster after creation
    Vec3D clusterVelocity_;
    //\brief mean cluster radius after creation.
    Mdouble meanClusterRadius_;

    // CENTRAL FORCE
    //\brief Value of damping modulus for velocity.
    Mdouble velocityDampingModulus_;

    //  DATA ANALYSIS
    // \brief Number of points used for computing internal structure.
    int nInternalStructurePoints_;

    // SPECIES
    //\brief particle species.
    LinearPlasticViscoelasticFrictionSpecies* particleSpecies_;


    // File
    //\brief bool used to define whether or not cluster data output must be created.
    bool isCdatOutputOn_;
    //\brief bool used to define whether or not overlap data output must be created.
    bool isOverlOutputOn_;
    //\brief bool used to define whether or not adjacency matrix output must be created.
    bool isAmatOutputOn_;
    //\brief bool used to define whether or not cluster internal structure output must be created.
    bool isIntStrucOutputOn_;
    //\brief bool used to define whether or not vtk output must be created.
    bool isVtkOutputOn_;
    //\brief bool used to define whether or not vtk output must be created.
    bool isRestartOutputOn_;
    //\brief bool used to define whether or not vtk output must be created.
    bool isFStatOutputOn_;
    //\brief bool used to define whether or not vtk output must be created.
    bool isEneOutputOn_;


    /*
     * ----------------------------------------------------------------------
     *                VARIABLES: never accessed by the user
     * ----------------------------------------------------------------------
     */


    // PARTICLES
    //\brief vector in which all radii will be stored after calculation.
    std::vector<Mdouble> radii_;
    //smallest radius
    Mdouble smallestRadius_;
    //\brief mass of the particle which has radius radiusParticle.
    Mdouble massParticle_;
    //\brief total volume of all particles.
    Mdouble totalParticleVolume_;

    // GEOMETRY
    //\brief size of the cubic domain.
    Mdouble boxSize_;
    //\brief center of mass.
    Vec3D centerOfMass_;

    // CONTACT RELATED
    //\brief adjacency matrix.
    std::vector< std::vector<int> > adjacencyMatrix_;
    //\brief mean coordination number.
    Mdouble meanCoordinationNumber_;
    //\brief maximum relative overlap.
    Mdouble maxRelativeOverlap_;
    //\brief mean relative overlap.
    Mdouble meanRelativeOverlap_;
    //\brief minimum relative overlap.
    Mdouble minRelativeOverlap_;
    //\brief number of total intra-cluster bonds.
    int nIntraClusterBonds_;

    // OUTPUT
    //\brief cluster data file.
    std::ofstream cdatFile_;
    //\brief cluster overlap file.
    std::ofstream overlFile_;
    //\brief gnuplot file.
    std::ofstream gnuplotFile_;
    //\brief adjacency matrix file.
    std::ofstream amatFile_;
    //\brief internal structure file.
    std::ofstream intStructFile_;
    //\brief output time of files and print time.
    Mdouble fileOutputTimeInterval_;

    // DATA ANALYSIS
    //\brief radius with which solid fraction is computed
    Mdouble radiusForSolidFraction_;
    //\brief solid fraction computed with the total particle volume and radiusForSolidFraction_.
    Mdouble solidFraction_;
    //\brief solid fraction computed with internal structure analysis.
    Mdouble solidFractionIntStruct_;

    // TIME
    // stage of the simulation: 1 compression, 2 decompression, 3 relaxation, 4 simulation ended.
    int stage_;
    //\brief time flag used for the stages duration.
    Mdouble t0_;
    //\brief final time.
    Mdouble clusterTimeMax_;

    // CENTRAL FORCE
    //\brief maximum force modulus applied on particles (this value is then multiplied by distance from force center).
    Mdouble maximumForceModulus_;
    //\brief force modulus applied on particles at a certain simulation time.
    Mdouble forceModulus_;
    //\brief time interval on which force is tuned (increased or decreased).
    Mdouble forceTuningInterval_;
    //\brief time interval on which velocity is tuned (increased or decreased).
    Mdouble velocityDampingInterval_;
    //\brief time duration of force tuning (i.e. duration of compression and decompression stages).
    Mdouble forceTuningDuration_;
    //\brief maximum possible time duration of dissipation (i.e. duration of dissipation if energy ratio
    //          tollerance not reached).
    Mdouble dissipationDuration_;
    //\brief Value of damping modulus for forceFactor.
    Mdouble forceDampingModulus_;

};
#endif