Microstructure.h

/*
 * Microstructure.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 MICROSTRUCTURE_H_
#define MICROSTRUCTURE_H_
 
#include "TrajectoryDiffusion.h"
 
struct neuron {
        double dx;      
        double dy;      
        double dz;      
        double x;       
        double y;       
        double z;       
        double r_a;     
        double r_m;     
};
 
class RNG;
 
class Microstructure {
public:
        Microstructure();
        virtual ~Microstructure();
 
        virtual void IndexObject(triple pos,  int &LastId ,int &shellid) {LastId=-1;shellid=-1;};
 
        virtual double GetD(int LastId=-1,int shellid=-1) {return m_D_external;};
 
        void SetExternalDiffusionConstant(double d) {m_D_external=d;};
 
        bool isInsideBox(triple pos) {return ((fabs(pos.x)<m_boxsize) & (fabs(pos.y)<m_boxsize) & (fabs(pos.z)<m_boxsize));};
 
        /*
         * maps a position outside of the box into it
         */
        triple PeriodicBoundary(triple trialpos);
 
        void SetBoxSize(double size) {m_boxsize=size;}
        double GetBoxSize() {return m_boxsize;}
 
protected:
        // microstructure is defined in box with [-m_boxsize..m_boxsize] in each direction
        double m_boxsize;
        double m_D_external;
 
        RNG* m_rng;
 
};
 
#endif /* MICROSTRUCTURE_H_ */