First attempt in solving an issue of dense packed internal pegs. They are r...

Samo Penic

2016-07-13 fc6f3ef0a9822f3d5f06d38e556dbb5f2e985f4a

 src/poly.c

@@ -6,7 +6,7 @@
#include"bond.h"
#include<math.h>
#include"energy.h"

#include"cell.h"
ts_bool poly_assign_filament_xi(ts_vesicle *vesicle, ts_tape *tape){
   ts_uint i;

@@ -55,7 +55,7 @@
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 i=0,j=0,k; //idx;
   ts_uint gvtxi;
   ts_double xnorm,ynorm,znorm,normlength;
   ts_double dphi,dh;
@@ -84,6 +84,10 @@
   if (vlist!=NULL){
   /* Make straight grafted poylmers normal to membrane (polymer brush). Dist. between poly vertices put to 1*/
      ts_int intpoly=vesicle->tape->internal_poly;
      ts_int cellidx;
      ts_double posX,posY,posZ,prevPosX,prevPosY,prevPosZ, phi,theta;
      ts_bool retval;
      ts_int l;
      for (i=0;i<poly_list->n;i++){
   
         xnorm=0.0;
@@ -102,10 +106,101 @@
         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;
         prevPosZ=poly_list->poly[i]->grafted_vtx->z;
         for (j=0;j<poly_list->poly[i]->vlist->n;j++){
            poly_list->poly[i]->vlist->vtx[j]->x = poly_list->poly[i]->grafted_vtx->x + xnorm*(ts_double)(j+1);
            poly_list->poly[i]->vlist->vtx[j]->y = poly_list->poly[i]->grafted_vtx->y + ynorm*(ts_double)(j+1);
            poly_list->poly[i]->vlist->vtx[j]->z = poly_list->poly[i]->grafted_vtx->z + znorm*(ts_double)(j+1);
            //trying to go towards normal
            posX=prevPosX+(ts_double)xnorm;
            posY=prevPosY+(ts_double)ynorm;
            posZ=prevPosZ+(ts_double)znorm;
            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]);
               //distance from neighbors
               //retval=TS_SUCCESS;
               /*for(k=0;k<poly_list->poly[i]->vlist->vtx[j]->neigh_no;k++){
                  dist=vtx_distance_sq(poly_list->poly[i]->vlist->vtx[j],poly_list->poly[i]->vlist->vtx[j]->neigh[k]);
                  if(dist<1.0 || dist>vesicle->dmax){
                     retval=TS_FAIL;
                     printf("dist_fail! %e\n", dist);
                  }
               }*/
               //if(retval!=TS_FAIL){
                  //check occupation number
                  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]);
                  break;
               }
               else{
            //      printf("%d %d Cannot put the vesicle here. Finding another position\n",i,j);
                  theta=drand48()*M_PI-M_PI/2;
                  phi=drand48()*2*M_PI;
                  posX=prevPosX+sin(phi)*cos(theta);
                  posY=prevPosY+sin(phi)*sin(theta);
                  posZ=prevPosZ+cos(theta);
                  //randomly change the normal.
               }
               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;

         //prepare starting position for building the polymeres
         posX=poly_list->poly[i]->grafted_vtx->x+xnorm;
         posY=poly_list->poly[i]->grafted_vtx->y+ynorm;
         posZ=poly_list->poly[i]->grafted_vtx->z+znorm;
			





                        break;
                     }
                  }
                  if(l>1000)
                     fatal("Cannot make internal polymeres. No space inside the vesicle?",1001);
               }
            }
            prevPosX=posX;
            prevPosY=posY;
            prevPosZ=posZ;
         }
      }
   }