Added most important missing files

Samo Penic

2014-04-28 460c2a326b332e1b3e03621970a1b48dfb872050

Added most important missing files

 src/constvol.c

New file
@@ -0,0 +1,160 @@
#include<stdlib.h>
#include<stdio.h>
#include<string.h>
#include<math.h>
#include "general.h"
#include "constvol.h"
#include "triangle.h"
#include "energy.h"
#include "vertex.h"
#include "cell.h"

ts_bool constvolume(ts_vesicle *vesicle, ts_vertex *vtx_avoid, ts_double Vol, ts_double *retEnergy, ts_vertex *vtx_moved, ts_vertex *vtx_backup){

    ts_uint vtxind,i,j;
    ts_uint Ntries=20;
    ts_vertex *backupvtx;
    ts_double Rv, dh, dvol, voldiff, oenergy,delta_energy;

    backupvtx=(ts_vertex *)calloc(sizeof(ts_vertex),10);

    for(i=0;i<Ntries;i++){
        vtxind=rand() % vesicle->vlist->n;
        vtx_moved=vesicle->vlist->vtx[vtxind];
        if(vtx_moved==vtx_avoid) continue;

        for(j=0;j<vtx_moved->neigh_no;j++){
            if(vtx_moved->neigh[j]==vtx_avoid) continue;
        }
        
        memcpy((void *)&backupvtx[0],(void *)vtx_moved,sizeof(ts_vertex));
        //move vertex in specified direction. first try, test move!

        Rv=sqrt(pow(vtx_moved->x,2)+pow(vtx_moved->y,2)+pow(vtx_moved->z,2));
        dh=2*Rv*vesicle->dmax/sqrt(3);
        vtx_moved->x=vtx_moved->x*(1-dh/Rv);
        vtx_moved->y=vtx_moved->y*(1-dh/Rv);
        vtx_moved->z=vtx_moved->z*(1-dh/Rv);

        //check for constraints
          if(constvolConstraintCheck(vesicle, vtx_moved)==TS_FAIL){
            vtx_moved=memcpy((void *)vtx_moved,(void *)&backupvtx[0],sizeof(ts_vertex));
            continue;
        }

        // All checks OK!

        // doing second and final move.
        for(j=0;j<vtx_moved->neigh_no;j++){
            memcpy((void *)&backupvtx[j+1],(void *)vtx_moved->neigh[j],sizeof(ts_vertex));
        }
        dvol=0.0;
        for(j=0;j<vtx_moved->tristar_no;j++){
            dvol-=vtx_moved->tristar[j]->volume;
            triangle_normal_vector(vtx_moved->tristar[j]);
            dvol+=vtx_moved->tristar[j]->volume;
        }

        voldiff=dvol-Vol;

        if(fabs(voldiff)/vesicle->volume < vesicle->tape->constvolprecision){
            //calculate energy, return change in energy...
             oenergy=vtx_moved->energy;
            energy_vertex(vtx_moved);
            delta_energy=vtx_moved->xk*(vtx_moved->energy - oenergy);
            //the same is done for neighbouring vertices
            for(i=0;i<vtx_moved->neigh_no;i++){
                oenergy=vtx_moved->neigh[i]->energy;
                energy_vertex(vtx_moved->neigh[i]);
                delta_energy+=vtx_moved->neigh[i]->xk*(vtx_moved->neigh[i]->energy-oenergy);
            }
            *retEnergy=delta_energy;
            vtx_backup=backupvtx;
            return TS_SUCCESS;
        }        
        //do it again ;)
        dh=Vol*dh/dvol;
        vtx_moved=memcpy((void *)vtx_moved,(void *)&backupvtx[0],sizeof(ts_vertex));
        vtx_moved->x=vtx_moved->x*(1-dh/Rv);
        vtx_moved->y=vtx_moved->y*(1-dh/Rv);
        vtx_moved->z=vtx_moved->z*(1-dh/Rv);
        //check for constraints
        if(constvolConstraintCheck(vesicle, vtx_moved)==TS_FAIL){
            for(j=0;j<vtx_moved->neigh_no;j++){
                memcpy((void *)vtx_moved->neigh[j],(void *)&backupvtx[j+1],sizeof(ts_vertex));
            }
            vtx_moved=memcpy((void *)vtx_moved,(void *)&backupvtx[0],sizeof(ts_vertex));
            continue;
        }

        voldiff=dvol-Vol;
        if(fabs(voldiff)/vesicle->volume < vesicle->tape->constvolprecision){
            //calculate energy, return change in energy...
            oenergy=vtx_moved->energy;
            energy_vertex(vtx_moved);
            delta_energy=vtx_moved->xk*(vtx_moved->energy - oenergy);
            //the same is done for neighbouring vertices
            for(i=0;i<vtx_moved->neigh_no;i++){
                oenergy=vtx_moved->neigh[i]->energy;
                energy_vertex(vtx_moved->neigh[i]);
                delta_energy+=vtx_moved->neigh[i]->xk*(vtx_moved->neigh[i]->energy-oenergy);
            }
            *retEnergy=delta_energy;
            vtx_backup=backupvtx;
            return TS_SUCCESS;
        }        


    }
    free(backupvtx);
    return TS_FAIL;
}


ts_bool constvolConstraintCheck(ts_vesicle *vesicle, ts_vertex *vtx){ 
        ts_uint i;
        ts_double dist;
        ts_uint cellidx;
        //distance with neighbours check
        for(i=0;i<vtx->neigh_no;i++){
            dist=vtx_distance_sq(vtx,vtx->neigh[i]);
            if(dist<1.0 || dist>vesicle->dmax) {
            return TS_FAIL;
            }
        }
        // Distance with grafted poly-vertex check:	
        if(vtx->grafted_poly!=NULL){
            dist=vtx_distance_sq(vtx,vtx->grafted_poly->vlist->vtx[0]);
            if(dist<1.0 || dist>vesicle->dmax) {
            return TS_FAIL;
            }
        }

        // Nucleus penetration check:
        if (vtx->x*vtx->x + vtx->y*vtx->y + vtx->z*vtx->z < vesicle->R_nucleus){
            return TS_FAIL;
        }

        //self avoidance check with distant vertices
        cellidx=vertex_self_avoidance(vesicle, vtx);
        //check occupation number
        return cell_occupation_number_and_internal_proximity(vesicle->clist,cellidx,vtx);
}



ts_bool constvolumerestore(ts_vertex *vtx_moved,ts_vertex *vtx_backup){
    ts_uint j;
    for(j=0;j<vtx_moved->neigh_no;j++){
                memcpy((void *)vtx_moved->neigh[j],(void *)&vtx_backup[j+1],sizeof(ts_vertex));
            }
            vtx_moved=memcpy((void *)vtx_moved,(void *)&vtx_backup[0],sizeof(ts_vertex));

    return TS_SUCCESS;
}

ts_bool constvolumeaccept(ts_vertex *vtx_moved, ts_vertex *vtx_backup){


    return TS_SUCCESS;
}

 src/constvol.h

New file
@@ -0,0 +1,8 @@
#ifndef _H_CONSTVOL
#define _H_CONSTVOL

ts_bool constvolume(ts_vesicle *vesicle, ts_vertex *vtx_avoid, ts_double Vol, ts_double *retEnergy, ts_vertex *vtx_moved, ts_vertex *vtx_backup);
ts_bool constvolConstraintCheck(ts_vesicle *vesicle, ts_vertex *vtx);
ts_bool constvolumerestore(ts_vertex *vtx_moved, ts_vertex *vtx_backup);
ts_bool constvolumeaccept(ts_vertex *vtx_moved, ts_vertex *vtx_backup);
#endif