Added most important missing files

Samo Penic

2014-04-28 460c2a326b332e1b3e03621970a1b48dfb872050

 src/poly.c

@@ -58,7 +58,6 @@
   ts_uint gvtxi;
   ts_double xnorm,ynorm,znorm,normlength;
   ts_double dphi,dh;
   ts_uint ji;

   // Grafting polymers:
   if (vlist!=NULL){
@@ -108,14 +107,29 @@
   else
   {
   /* Make filaments inside the vesicle. Helix with radius... Dist. between poly vertices put to 1*/
      dphi = 2.0*asin(1.0/2.0/vesicle->R_nucleus)*1.01;
      dh = dphi/2.0/M_PI*1.01;
   ts_double a,R,H,tantheta,h,r,phi,A0=1.2;

      a = A0*(ts_double)vesicle->nshell;
      R = A0*((ts_double)vesicle->nshell)/(2.0*sin(M_PI/5.0));
      H = sqrt(a*a - R*R);
      tantheta = sqrt(R*R - a*a/4.0)/H;
		
      h = -H + sqrt(vesicle->clist->dmin_interspecies)*1.5;
      r = (H-fabs(h))*tantheta - sqrt(vesicle->clist->dmin_interspecies)*1.5;
      dphi = 2.0*asin(1.0/2.0/r)*1.001;
      dh = dphi/2.0/M_PI*1.001;
      phi=0.0;
      for(i=0;i<poly_list->n;i++){
         for (j=0;j<poly_list->poly[i]->vlist->n;j++){
            ji = j + i*poly_list->poly[i]->vlist->n;
            poly_list->poly[i]->vlist->vtx[j]->x = vesicle->R_nucleus*cos(ji*dphi);
            poly_list->poly[i]->vlist->vtx[j]->y = vesicle->R_nucleus*sin(ji*dphi);
            poly_list->poly[i]->vlist->vtx[j]->z = ji*dh - (dh*poly_list->n*poly_list->poly[i]->vlist->n/2.0);
            h = h + dh;
            r = (H-fabs(h))*tantheta - sqrt(vesicle->clist->dmin_interspecies)*1.5;
            dphi = 2.0*asin(1.0/2.0/r)*1.001;
            dh = dphi/2.0/M_PI*1.001;
            phi+=dphi;
            //ji = j + i*poly_list->poly[i]->vlist->n;
            poly_list->poly[i]->vlist->vtx[j]->x = r*cos(phi);
            poly_list->poly[i]->vlist->vtx[j]->y = r*sin(phi);
            poly_list->poly[i]->vlist->vtx[j]->z = h;// ji*dh - (dh*poly_list->n*poly_list->poly[i]->vlist->n/2.0);
         }
      }
   }