Merge branch 'master' into plugins

Samo Penic

2019-02-27 d2f3609e9ecec5ec8dc02a992a6ec98e28ca9c6d

 src/initial_distribution.c

@@ -44,6 +44,7 @@
   vesicle=initial_distribution_dipyramid(tape->nshell,tape->ncxmax,tape->ncymax,tape->nczmax,tape->stepsize);
       vesicle->tape=tape;
   set_vesicle_values_from_tape(vesicle);
      initial_population_with_c0(vesicle,tape);
   return vesicle;
}

@@ -100,7 +101,7 @@
   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? */
   vesicle->clist->max_occupancy=16; /* hard coded max occupancy? */

   vesicle->pressure= tape->pressure;
   vesicle->pswitch=tape->pswitch;
@@ -111,26 +112,37 @@
        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){
   int rndvtx,i,j;
   if(tape->number_of_vertices_with_c0>0){
//      ts_fprintf(stderr,"Setting values for spontaneous curvature as defined in tape\n");
      j=0;
      for(i=0;i<tape->number_of_vertices_with_c0;i++){
         rndvtx=rand() % vesicle->vlist->n;
         if(fabs(vesicle->vlist->vtx[rndvtx]->c-tape->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=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);
      }
   }
   return TS_SUCCESS;
}


ts_bool pentagonal_dipyramid_vertex_distribution(ts_vertex_list *vlist){