Improved the code, still breaks

Samo Penic

2016-07-13 e2db4a0e170272935ccc8532bc245938aadc36fc

Improved the code, still breaks

 src/poly.c

@@ -53,44 +53,15 @@
}


ts_poly_list *init_poly_list(ts_uint n_poly, ts_uint n_mono, ts_vertex_list *vlist, ts_vesicle *vesicle){
    ts_poly_list *poly_list=(ts_poly_list *)calloc(1,sizeof(ts_poly_list));
    poly_list->poly    = (ts_poly **)calloc(n_poly,sizeof(ts_poly *));
    ts_uint i=0,j=0,k; //idx;
    ts_uint gvtxi;
    ts_double xnorm,ynorm,znorm,normlength;
    ts_double dphi,dh;
    cell_occupation(vesicle); //needed for evading the membrane
    // Grafting polymers:
    if (vlist!=NULL){
        if (n_poly > vlist->n){fatal("Number of polymers larger than numbero f vertices on a vesicle.",310);}
	
        while(i<n_poly){
            gvtxi = rand() % vlist->n;
            if (vlist->vtx[gvtxi]->grafted_poly == NULL){
            poly_list->poly[i] = init_poly(n_mono, vlist->vtx[gvtxi]);
            i++;
            }
        }
    }
    else
    {
        for(i=0;i<n_poly;i++){
            poly_list->poly[i] = init_poly(n_mono, NULL);
        }
    }

    poly_list->n = n_poly;

    if (vlist!=NULL){
ts_bool poly_initial_distribution(ts_poly_list *poly_list, ts_int i, ts_vesicle *vesicle){
    /* Make straight grafted poylmers normal to membrane (polymer brush). Dist. between poly vertices put to 1*/
        ts_double xnorm,ynorm,znorm,normlength;
        ts_int intpoly=vesicle->tape->internal_poly;
        ts_int cellidx;
        ts_double posX,posY,posZ,prevPosX,prevPosY,prevPosZ, phi,costheta,sintheta;
        ts_bool retval;
        ts_int l;
        for (i=0;i<poly_list->n;i++){
	
        ts_int j,k,l,m;
            xnorm=0.0;
            ynorm=0.0;
            znorm=0.0;
@@ -106,7 +77,6 @@
            xnorm=xnorm/normlength;
            ynorm=ynorm/normlength;
            znorm=znorm/normlength;

            //prepare starting position for building the polymeres
            prevPosX=poly_list->poly[i]->grafted_vtx->x;
            prevPosY=poly_list->poly[i]->grafted_vtx->y;
@@ -123,94 +93,104 @@
                //}
                //trying to go towards normal
                k=0;
                l=0;
                while(1){
                    poly_list->poly[i]->vlist->vtx[j]->x = posX;
                    poly_list->poly[i]->vlist->vtx[j]->y = posY;
                    poly_list->poly[i]->vlist->vtx[j]->z = posZ;
                    cellidx=vertex_self_avoidance(vesicle, poly_list->poly[i]->vlist->vtx[j]);
                    retval=cell_occupation_number_and_internal_proximity(vesicle->clist,cellidx,poly_list->poly[i]->vlist->vtx[j]);

                    if(retval==TS_SUCCESS){
                        //retval=cell_add_vertex(vesicle->clist->cell[cellidx],poly_list->poly[i]->vlist->vtx[j]);
                        retval=cell_add_vertex(vesicle->clist->cell[cellidx],poly_list->poly[i]->vlist->vtx[j]);
                        break;
                    }
                    else{
                    //    printf("%d %d Cannot put the vertex here. Finding another position\n",i,j);
                        //randomly change the direction.
                        do{
                        costheta=2.0*drand48()-1.0;
                        sintheta=sqrt(1-pow(costheta,2));
                        phi=drand48()*2.0*M_PI;
                        if(j==0){
                        //for special cases, when we are on the edge of bipytamid  the distance od dmin_interspecies is not enough
                        posX=prevPosX+vesicle->dmax*sintheta*cos(phi);
                        posY=prevPosY+vesicle->dmax*sintheta*sin(phi);
                        posZ=prevPosZ+vesicle->dmax*costheta;


                        } else {
                        posX=prevPosX+vesicle->clist->dmin_interspecies*sintheta*cos(phi);
                        posY=prevPosY+vesicle->clist->dmin_interspecies*sintheta*sin(phi);
                        posZ=prevPosZ+vesicle->clist->dmin_interspecies*costheta;
                        }
                    //    if(j>0) break;
                    //    if((xnorm*sintheta*cos(phi)+ynorm*sintheta*sin(phi)+znorm*costheta)<0.0 && j==0) break;
                        }
                    //    while(j==0);
                        m=0;
                        //we must move first vertex into the vesicle if the normal is in or out of the vesicle if the normal is out
                        do{
                            costheta=2.0*drand48()-1.0;
                            sintheta=sqrt(1-pow(costheta,2));
                            phi=drand48()*2.0*M_PI;
                            if(j==0){
                        //for special cases, when we are on the edge of bipyramid  the distance od dmin_interspecies is not enough
                                posX=prevPosX+vesicle->dmax*sintheta*cos(phi);
                                posY=prevPosY+vesicle->dmax*sintheta*sin(phi);
                                posZ=prevPosZ+vesicle->dmax*costheta;

                            } else {
                                posX=prevPosX+vesicle->clist->dmin_interspecies*sintheta*cos(phi);
                                posY=prevPosY+vesicle->clist->dmin_interspecies*sintheta*sin(phi);
                                posZ=prevPosZ+vesicle->clist->dmin_interspecies*costheta;
                            }
                            m++;
                            if(m>1000) {
                                k=9999; //break also ot of the outer loop
                                printf("was here\n");
                                break;
                            }
                        }
                        while((xnorm*(poly_list->poly[i]->grafted_vtx->x-posX)+ynorm*(poly_list->poly[i]->grafted_vtx->y-posY)+znorm*(poly_list->poly[i]->grafted_vtx->z-posZ))>0.0 && j==0);
                    }
                    k++;
                    if(k>1000){
                        //lets choose another grafting vertex;
                        while(1){
                            gvtxi = rand() % vesicle->vlist->n;
                            if (vesicle->vlist->vtx[gvtxi]->grafted_poly == NULL){
                                ts_fprintf(stdout,"Found new potential grafting vertex %d for poly %d\n",gvtxi,i);
                                poly_list->poly[i]->grafted_vtx->grafted_poly=NULL;
                                poly_list->poly[i]->grafted_vtx = vesicle->vlist->vtx[gvtxi];
                                vesicle->vlist->vtx[gvtxi]->grafted_poly = poly_list->poly[i];
                                l++;
                                k=0;
                                xnorm=0.0;
                                ynorm=0.0;
                                znorm=0.0;
                                int o;
                                for (o=0;o<poly_list->poly[i]->grafted_vtx->tristar_no;o++){
                                    xnorm-=poly_list->poly[i]->grafted_vtx->tristar[o]->xnorm;
                                    ynorm-=poly_list->poly[i]->grafted_vtx->tristar[o]->ynorm;
                                    znorm-=poly_list->poly[i]->grafted_vtx->tristar[o]->znorm;	
                                }
                                normlength=sqrt(xnorm*xnorm+ynorm*ynorm+znorm*znorm);
                                if(intpoly && i%2){
                                    normlength=-normlength;
                                }
                                xnorm=xnorm/normlength;
                                ynorm=ynorm/normlength;
                                znorm=znorm/normlength;
                                prevPosX=poly_list->poly[i]->grafted_vtx->x;
                                prevPosY=poly_list->poly[i]->grafted_vtx->y;
                                prevPosZ=poly_list->poly[i]->grafted_vtx->z;
                                //prepare starting position for building the polymeres
                                posX=prevPosX+xnorm*(vesicle->clist->dmin_interspecies);
                                posY=prevPosY+ynorm*(vesicle->clist->dmin_interspecies);
                                posZ=prevPosZ+znorm*(vesicle->clist->dmin_interspecies);
                                break;
                            }
                        //undo changes to the cell
                        for(l=0;l<j-1;l++){
                            cellidx=vertex_self_avoidance(vesicle, poly_list->poly[i]->vlist->vtx[l]);
                            cell_remove_vertex(vesicle->clist->cell[cellidx],poly_list->poly[i]->vlist->vtx[l]);
                        }
                        if(l>1000)
                            fatal("Cannot make internal polymeres. No space inside the vesicle?",1001);
                        return TS_FAIL;
                    }
                }
                prevPosX=posX;
                prevPosY=posY;
                prevPosZ=posZ;
            }
    printf("did it\n");
    return TS_SUCCESS;

}


ts_poly_list *init_poly_list(ts_uint n_poly, ts_uint n_mono, ts_vertex_list *vlist, ts_vesicle *vesicle){
    ts_poly_list *poly_list=(ts_poly_list *)calloc(1,sizeof(ts_poly_list));
    poly_list->poly    = (ts_poly **)calloc(n_poly,sizeof(ts_poly *));
    ts_uint i=0,j=0; //idx;
    ts_uint gvtxi;
    ts_bool retval;
    ts_double dphi,dh;
    cell_occupation(vesicle); //needed for evading the membrane
    // Grafting polymers:
    if (vlist!=NULL){
        if (n_poly > vlist->n){fatal("Number of polymers larger than numbero f vertices on a vesicle.",310);}
	
        while(i<n_poly){
            gvtxi = rand() % vlist->n;
            if (vlist->vtx[gvtxi]->grafted_poly == NULL){
                poly_list->poly[i] = init_poly(n_mono, vlist->vtx[gvtxi]);
                retval=poly_initial_distribution(poly_list, i, vesicle);
                if(retval==TS_FAIL){
                    ts_fprintf(stdout,"Found new potential grafting vertex %d for poly %d\n",gvtxi,i);
                }
                else {
                    i++;
                }
            }
        }
    }
    else
    {
        for(i=0;i<n_poly;i++){
            poly_list->poly[i] = init_poly(n_mono, NULL);
        }
    }

    poly_list->n = n_poly;

    if (vlist!=NULL){
    }
    else
    {
    /* Make filaments inside the vesicle. Helix with radius... Dist. between poly vertices put to 1*/
    ts_double a,R,H,tantheta,h,r,phi,A0=1.2;


 src/tape

@@ -25,7 +25,7 @@

####### Polymer (brush) definitions ###########
# npoly is a number of polymers attached to npoly distinct vertices on vesicle
npoly=30
npoly=400
# nmono is a number of monomers in each polymer
nmono=10
# Spring constant between monomers of the polymer