Code for incremental adding of inclusions done

Samo Penic

2020-04-26 3006183b769f2e126b1a96e6bf697c2b7f657df7

 src/initial_distribution.c

@@ -43,7 +43,10 @@

   vesicle=initial_distribution_dipyramid(tape->nshell,tape->ncxmax,tape->ncymax,tape->nczmax,tape->stepsize);
       vesicle->tape=tape;
   vesicle->clist->dmin_interspecies = tape->dmin_interspecies*tape->dmin_interspecies;
   vesicle->poly_list=init_poly_list(tape->npoly,tape->nmono, vesicle->vlist, vesicle);
   set_vesicle_values_from_tape(vesicle);
      initial_population_with_c0(vesicle,tape);
   return vesicle;
}

@@ -58,7 +61,7 @@
   vesicle->clist->dmin_interspecies = tape->dmin_interspecies*tape->dmin_interspecies;

   //Initialize grafted polymers (brush):
   vesicle->poly_list=init_poly_list(tape->npoly,tape->nmono, vesicle->vlist, vesicle);
   //vesicle->poly_list=init_poly_list(tape->npoly,tape->nmono, vesicle->vlist, vesicle);
   vesicle->spring_constant=tape->kspring;
   poly_assign_spring_const(vesicle);

@@ -100,7 +103,8 @@
   vesicle->clist->ncmax[0]=tape->ncxmax;
   vesicle->clist->ncmax[1]=tape->ncymax;
   vesicle->clist->ncmax[2]=tape->nczmax;
   vesicle->clist->max_occupancy=8; /* hard coded max occupancy? */
//THIS IS NOW HARDCODED IN CELL.C
//   vesicle->clist->max_occupancy=16; /* hard coded max occupancy? */

   vesicle->pressure= tape->pressure;
   vesicle->pswitch=tape->pswitch;
@@ -111,27 +115,47 @@
        vesicle->sphHarmonics=NULL;
    }

   int rndvtx;
   if(tape->number_of_vertices_with_c0>0){
      ts_fprintf(stderr,"Setting values for spontaneous curvature as defined in tape\n");
      for(i=0;i<tape->number_of_vertices_with_c0;i++){
         rndvtx=rand() % vesicle->vlist->n;
         vesicle->vlist->vtx[rndvtx]->c=tape->c0;
      }
      mean_curvature_and_energy(vesicle);
      if(fabs(tape->w)>1e-16){ //if nonzero energy
         ts_fprintf(stderr,"Setting attraction between vertices with spontaneous curvature\n");
         sweep_attraction_bond_energy(vesicle);
      }
   }
    
   vesicle->tlist->a0=sqrt(3)/4*pow((vesicle->tape->dmax+1.0)/2.0,2);  
    return TS_SUCCESS;

}


ts_bool initial_population_with_c0(ts_vesicle *vesicle, ts_tape *tape){
// OVERRIDE! JUST FOR TEST BRANCH!!!
// WARNING !!!!
// WARNING !!!!
// WARNING !!!!
   return TS_SUCCESS;
   if(tape->number_of_vertices_with_c0>0){
//      ts_fprintf(stderr,"Setting values for spontaneous curvature as defined in tape\n");
      add_vertices_with_c0(vesicle, tape->number_of_vertices_with_c0, tape->c0, tape->w);
   }
   return TS_SUCCESS;
}

ts_bool add_vertices_with_c0(ts_vesicle *vesicle, ts_int n, ts_double c0, ts_double w){
      ts_int rndvtx,i,j=0;
      for(i=0;i<n;i++){
         rndvtx=rand() % vesicle->vlist->n;
         if(fabs(vesicle->vlist->vtx[rndvtx]->c-c0)<1e-15){
            j++;
            i--;
            if(j>10*vesicle->vlist->n){
               fatal("cannot populate vesicle with vertices with spontaneous curvature. Too many spontaneous curvature vertices?",100);
            }
            continue;
         }
         vesicle->vlist->vtx[rndvtx]->c=c0;
      }
      mean_curvature_and_energy(vesicle);
      if(fabs(w)>1e-16){ //if nonzero energy
//         ts_fprintf(stderr,"Setting attraction between vertices with spontaneous curvature\n");
         sweep_attraction_bond_energy(vesicle);
      }
   return TS_SUCCESS;

}

ts_bool pentagonal_dipyramid_vertex_distribution(ts_vertex_list *vlist){
   /* Some often used relations */