Many changes to the code to allow internal pegs

Samo Penic

2016-07-13 90882f51387b945bc0f660d8b12200b2f48e80fa

 src/poly.c

@@ -7,6 +7,7 @@
#include<math.h>
#include"energy.h"
#include"cell.h"
#include"frame.h"
ts_bool poly_assign_filament_xi(ts_vesicle *vesicle, ts_tape *tape){
   ts_uint i;

@@ -47,7 +48,7 @@
   poly->blist->bond[i]->bond_length=sqrt(vtx_distance_sq(poly->blist->bond[i]->vtx1,poly->blist->bond[i]->vtx2));
   bond_energy(poly->blist->bond[i],poly);
   }

   vertex_list_assign_id(poly->vlist,TS_ID_FILAMENT);
   return poly;
}

@@ -59,7 +60,7 @@
   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);}
@@ -85,7 +86,7 @@
   /* 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_double posX,posY,posZ,prevPosX,prevPosY,prevPosZ, phi,costheta,sintheta;
      ts_bool retval;
      ts_int l;
      for (i=0;i<poly_list->n;i++){
@@ -111,10 +112,16 @@
         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++){
            //if(j==0){
               posX=prevPosX+xnorm*(vesicle->clist->dmin_interspecies);
               posY=prevPosY+ynorm*(vesicle->clist->dmin_interspecies);
               posZ=prevPosZ+znorm*(vesicle->clist->dmin_interspecies);
            //}else{
            //   posX=prevPosX+xnorm;
            //   posY=prevPosY+ynorm;
            //   posZ=prevPosZ+znorm;
            //}
            //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){
@@ -122,31 +129,37 @@
               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]);
               //}
               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 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.
               //   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);
                  //we must move first vertex into the vesicle if the normal is in or out of the vesicle if the normal is out
                  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){
@@ -160,37 +173,29 @@
                        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;
			





                        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;
                     }
                  }
@@ -244,7 +249,7 @@
      }
   }
*/

	
   return poly_list;
}