copss_point_particle_system.h

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// Copyright (C) 2015-2016 Xujun Zhao, Jiyuan Li, Xikai Jiang

// This code is free software; you can redistribute it and/or
// modify it under the terms of the GNU General Public
// License as published by the Free Software Foundation; either
// version 2.1 of the License, or (at your option) any later version.


// This code is distributed in the hope that it will be useful,
// but WITHOUT ANY WARRANTY; without even the implied warranty of
// MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
// Lesser General Public License for more details.


// You should have received a copy of the GNU General Public
// License along with this code; if not, write to the Free Software
// Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA  02111-1307  USA
#pragma once

#include "../copss.h"
#include "../polymer_chain.h"

using std::cout;
using std::endl;
using std::string;

namespace libMesh{

class CopssPointParticleSystem : public Copss
{
public:
    
    CopssPointParticleSystem (CopssInit& init);

    ~CopssPointParticleSystem();

    // integrator
    void run(EquationSystems& equation_systems) override;

protected:
    std::string point_particle_model;
    // ===========for beads and polymer chains
    unsigned int Nb; // total # of beads
    unsigned int Ns; // total # of springs per Chain
    unsigned int nBonds; // total # of springs/bonds
    // ===========for polymer chains
    unsigned int nChains; // total # of chains
    Real bk; // Kuhn length (um)
    Real Nks; // # of Kuhn length per Chain
    Real Ss2; // (um^2)
    Real q0; //maximum spring length (um)
    Real chain_length; // contour length of the spring (um)
    Real Dc; // Diffusivity of the chain (um^2/s)

    // extra parameters for dynamic process
    Real max_spring_len;
    bool chain_broken;

    // override read_particle_parameters() function in Copss class
    void read_particle_info () override;

    // read ggem and ibm info
    void read_ggem_info () override;
    
    // create objects, polymer chains
    void create_object() override;

    // create object mesh
    void create_object_mesh() override;

    // attach object mesh to system
    void attach_object_mesh(PMLinearImplicitSystem& system) override;

    // set parameters for equations systems
    void set_parameters(EquationSystems& equation_systems) override;

    // update object due to PBC after check_wall()
    void update_object();
        
    // write object to output file
    void write_object(unsigned int step_id) override;



private:

    PolymerChain* polymer_chain;
    //std::unique_ptr<PolymerChain> polymer_chain;

    //std::unique_ptr<PointMesh<3> > point_mesh; 



};


}