TrajectoryDiffusion.h

/*
 * TrajectoryDiffusion.h
 *
 *  Created on: Dec 10, 2009
 *      Author: dpflug
 */
 
 
/*
 *  JEMRIS Copyright (C) 
 *                        2006-2025  Tony Stoecker
 *                        2007-2018  Kaveh Vahedipour
 *                        2009-2019  Daniel Pflugfelder
 *                                  
 *
 *  This program 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 of the License, or
 *  (at your option) any later version.
 *
 *  This program 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 General Public License for more details.
 *
 *  You should have received a copy of the GNU General Public License
 *  along with this program; if not, write to the Free Software
 *  Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA
 */
 
#ifndef TRAJECTORYDIFFUSION_H_
#define TRAJECTORYDIFFUSION_H_
 
#include "TrajectoryInterface.h"
#include "rng.h"
#include "XMLIO.h"
 
 
enum modes{BOTH, INTERNAL, EXTERNAL};
 
using namespace std;
 
class Microstructure;
 
struct triple {
        double x,y,z;
};
 
class TrajectoryDiffusion: public TrajectoryInterface {
public:
        TrajectoryDiffusion();
        virtual ~TrajectoryDiffusion();
 
//load diffusion definition file
        virtual void LoadFile(string filename) ;
 
        virtual void GetValueDerived(double time, double *pos);
 
        virtual void UpdateTrajectory(bool init);
 
        void DumpTrajectory(string filename);
 
private:
 
        // xml access functions
        string                  GetAttr         (DOMElement* element, string key);
        DOMElement*     GetElem                 (string name);
 
        void GenerateDiffusionTrajectory();
        void CalcY();                                           // calc information for cubic spline interpolation.
 
        void SetSeed(long seed);
 
        Microstructure *m_microstruct;
 
        vector<triple> m_pos;
        // vector for cubic splines interpolation:
        vector<triple> m_y;
 
        unsigned long m_seed;
        RNG* m_rng;
 
        double m_timestep;
        long m_max_timesteps;
 
        // mode ==0 simulate internal and external, mode ==1 only internal, mode == 2 only external
        modes m_mode;
 
        vector<int> m_dump_index; //dump the trajectory of these spins
 
        int m_diff_dimension;   // flag for 3-dimensional, 2-dim or 1-dim diffusion; default: 3-dim
        void ProjectPosition(triple &pos, triple dir);
 
        // variables for xml reader:
        DOMTreeErrorReporter*   m_domtree_error_rep;
        XMLIO*                  m_xio;
        DOMDocument*            m_dom_doc;
 
 
};
 
#endif /* TRAJECTORYDIFFUSION_H_ */