Biomechanical Joint Model  Author: Anderson Maciel

---

comemoleculestissue.h

Go to the documentation of this file.

/***************************************************************************
 *   Copyright (C) 2002 by Anderson Maciel                                 *
 *   andi.maciel@gmail.com                                                 *
 *                                                                         *
 *   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.,                                       *
 *   59 Temple Place - Suite 330, Boston, MA  02111-1307, USA.             *
 **************************************************************************/

//
//  PROJECT.....: CO-ME
//  RESPONSIBLE.: 
//
//  AUTHOR......: Anderson Maciel
//  DATE........: October/24/2002
//  DESCRIPTION.: Class declaration.
//

#ifndef __COME_MOLECULESTISSUE_H        
#define __COME_MOLECULESTISSUE_H        


#include <general/come.h>
#include <bio/comemolecule.h>
#include <bio/comemoleculeschain.h>


class COME_MoleculesTissue : public COME {

protected:
        list<COME_Molecule*>    shape;
        double                          radiusAverage;
        double                          mass;
        int                                     averageNumConnectionsPerMolecule;
        float                                   accu;
        double                          simTime;
        
        //void  updateSurface( double skinSphere, double stiff, double resolution );
        COME_Vector3D *dymv, *dyma, *dytv, *dyta, *ytp, *ytv, *gpuForces;


public:
        COME_MoleculesTissue();
        virtual ~COME_MoleculesTissue();

        list<COME_Molecule*>*   getShape();

        void    setRadiusAverage( double radiusN );
        void    setMass( double massN );
        void    updateAverageNumConnections();

        void    addMolecule( COME_Molecule *moleculeN );
        void    addMolecule( COME_Molecule *moleculeN, double minDdist );
        bool    updateEuler( double timestep, double simClock, string fileNameToSaveDeformation );
        bool    update( double timestep, double simClock, string fileNameToSaveDeformation );
        //void  updateSurface( bool regenerate );
        void    initForSimulation();
        void    makeAllLocalFrames();
        /* visco */ void        flow( double timestep );

        COME_Molecule*  nearestTo( COME_Point3D point );
        void            getEnvelop( COME_Point3D& mins, COME_Point3D& maxs );
        double          getMass();
        int                     getAverageNumConnections();
        double          getRadiusAverage();
        COME_Point3D    getMassCenter();
        COME_Force      getGPUForce( int i );
        void            recalculateAllSpringConstants( int mode, double currTime ); 
        void            setSurfaceMolecules();
        bool            isTooClose( COME_Point3D currentPoint, double distance );

        void    setMoleculesMaterial( COME_Material* newMaterial );
        void    setMoleculesDensity( double densityN );
        void    setMoleculesElasticity( double elasticityN );
        void    setMoleculesFrictionConst( double frictionN );
        
        COME_Material* getMoleculesMaterial();

        double  getDensity();
        double  getElasticity();
        double  getFrictionConst();
        double  getTopStress();
        void    checkInitialPositions();
        void    resetInitialPositions();

        // Auxiliary to test numerical method to configure spring k's.
        COME_MoleculesChain chain;

        
        // for offline simulation
        vector<COME_Point3D*>   deformation;
        vector<double*>         deformationStresses;
        vector<double*>         deformationStrains;
        void                    loadDeformationFile( string fileName );
        void                    saveDeformationFile( int fileMode  );
        
        // transforms
        void    scale( double factorx, double factory, double factorz );
        void    translate( double dx, double dy, double dz );
        void    rotate( double rx, double ry, double rz );
        void    transform( COME_Matrix M );
        void    transform( COME_Matrix M, COME_Matrix MP );
        
        void    scaleNominals( double factor );
};

#endif // __COME_MOLECULESTISSUE_H

---